Re: [aroma.affymetrix] Error with process function: package sfit not found
Hi.
The 'sfit' package is special, preventing me from submitting it to
CRAN without a major rewrite. Because of this, it's not available
from CRAN and there's no pre-built Windows binary for it either, which
is what you're running into here.
I basically have to manually build Windows binaries and make them
available elsewhere, which I've forgotten for a while now. I've made
one for R 4.0.x available, assuming that's what you're running. I've updated
https://github.com/HenrikBengtsson/sfit
with instructions for installing 'sfit', including on Windows.
Let me know if it works,
Henrik
On Thu, Nov 12, 2020 at 12:44 PM Mirko Pisati wrote:
>
> Hi ,
> I have a problem with the process function where it says csC
> csC <- process (acc, verbose = verbose)
> print (csC).
> Failed with error: ‘there is no package called ‘sfit’’
> I have copy number data of a geo dateset and i want to process it with this
> package. I saw the Vignette page of the package and I followed all the setup
> steps step by step.
> R gives me the error in which it says it does not find the sfit package, if I
> try to install it from outside with different functions, they all tell me
> that the package is not found or not available for my version of r WHICH is
> 4.0.3 , the last.
> > source('http://callr.org/install#HenrikBengtsson/sfit')
> > install.packages("remotes")
> > remotes::install_github("HenrikBengtsson/sfit")
> Error in file (filename, "r", encoding = encoding):
> I can't open this connection
> Also: Warning message:
> In file (filename, "r", encoding = encoding):
> cannot open URL 'http://callr.org/install#HenrikBengtsson/sfit': HTTP
> status was '400 Bad Request'
> > remotes::install_github("HenrikBengtsson/sfit")
> Downloading GitHub repo HenrikBengtsson/sfit@HEAD
> √ checking for file
> 'C:\Users\mirko\AppData\Local\Temp\Rtmp0U19NX\remotes46d42edc29b\HenrikBengtsson-sfit-dd85e19/DESCRIPTION'
> (736ms)
> - preparing 'sfit':
> √ checking DESCRIPTION meta-information ...
> - cleaning src
> - checking for LF line-endings in source and make files and shell scripts
> (637ms)
> - checking for empty or unneeded directories
> - building 'sfit_0.3.1.tar.gz'
>
> Installing package into ‘C:/Users/mirko/Documents/R/win-library/4.0’
> (as ‘lib’ is unspecified)
> * installing *source* package 'sfit' ...
> ** using staged installation
> ** libs
> running 'src/Makefile.win' ...
> cc-c -o cfit.o cfit.c
> make: cc: Command not found
> make: *** [: cfit.o] Error 127
> ERROR: compilation failed for package 'sfit'
> * removing 'C:/Users/mirko/Documents/R/win-library/4.0/sfit'
> Errore: Failed to install 'sfit' from GitHub:
> (contertito da avviso) installation of package
> ‘C:/Users/mirko/AppData/Local/Temp/Rtmp0U19NX/file46d4153539da/sfit_0.3.1.tar.gz’
> had non-zero exit status
> > sessionInfo()
> R version 4.0.3 (2020-10-10)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 10 x64 (build 19041)
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252
> LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C
> LC_TIME=Italian_Italy.1252
>
> attached base packages:
> [1] parallel stats4stats graphics grDevices utils datasets
> methods base
>
> other attached packages:
> [1] SummarizedExperiment_1.18.2 DelayedArray_0.14.1
> matrixStats_0.57.0 Biobase_2.48.0 GenomicRanges_1.40.0
> [6] GenomeInfoDb_1.24.2 IRanges_2.22.2 S4Vectors_0.26.1
> BiocGenerics_0.34.0
>
> loaded via a namespace (and not attached):
> [1] compiler_4.0.3 BiocManager_1.30.10XVector_0.28.0
> prettyunits_1.1.1 R.methodsS3_1.8.1 bitops_1.0-6
> [7] R.utils_2.10.1 remotes_2.2.0 tools_4.0.3
> zlibbioc_1.34.0pkgbuild_1.1.0 preprocessCore_1.50.0
> [13] lattice_0.20-41Matrix_1.2-18 cli_2.1.0
> rstudioapi_0.11curl_4.3 GenomeInfoDbData_1.2.3
> [19] withr_2.3.0rprojroot_1.3-2grid_4.0.3
> glue_1.4.2 R6_2.4.1 processx_3.4.4
> [25] fansi_0.4.1callr_3.5.1backports_1.1.10
> ps_1.4.0 assertthat_0.2.1 affy_1.66.0
> [31] RCurl_1.98-1.2 crayon_1.3.4 affyio_1.58.0
> R.oo_1.24.0
> Please, can someone help me ?
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
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>
> ---
> You recei
Re: [aroma.affymetrix] Re: CalMaTe model fitting error
Hi. This is a hard-to-troubleshoot problem. This could be due to one
or more arrays having weak/noisy signals, or possibly even being
corrupt.
As a first small step, I've created feature request
https://github.com/HenrikBengtsson/calmate/issues/7. When that is in
place, one can narrow down the problematic data and make the estimator
more robust.
/Henrik
On Thu, Sep 13, 2018 at 7:37 AM wrote:
>
> I forgot the traceback:
>
> traceback()
> 11: stop("singular matrix 'a' in solve")
> 10: qr.solve(t(TR) * wgths^2, t(Genotypes) * wgths^2)
> 9: fitCalMaTeMedians(dataInit, references = references, fB1 = fB1,
>fB2 = fB2)
> 8: fitFcn(Cjj, references = references, ...)
> 7: calmateByThetaAB.array(theta, references = references, ..., verbose =
> verbose)
> 6: calmateByThetaAB(theta, references = references, ..., verbose = verbose)
>
>
> Am Donnerstag, 13. September 2018 16:35:14 UTC+2 schrieb
> thomas.g...@merckgroup.com:
>>
>> Hello,
>>
>> I am using CALMATE 0.12.1 to improve ASCN for a 1213 sample SNP6 data set
>> without reference samples.
>> I run the analysis on a 32core 156Gb main memory server. When CALMATE is
>> fitting the model the following error occurs:
>>
>> ...
>> setOption(aromaSettings, "memory/ram", 10.0)
>> ...
>> cmt <- CalMaTeCalibration(dsNList)
>> dsCList <- process(cmt, verbose=verbose)
>> ...
>> 20180913 09:41:43| Fitting CalMaTe...
>> 20180913 09:41:43| Algorithm flavor: v2
>> 20180913 09:41:43| Number of SNPs: 515251
>> 20180913 09:41:43| Number of SNPs left: 515251, 514751, 514251, 513751,
>> 513251, 512751, 512251, 511751, 511251, 510751, 510251, 509751, 509251,
>> 508751, 508251, 507751, 507251, 506751, 506251, 505751, 505251, 504751,
>> 504251, 503751, 503251, 502751, 502251, 501751, 501251, 500751, 500251,
>> 499751, 49925
>> ...
>> 288251, 287751, 287251, 286751, 286251, 285751, 285251, 284751, 284251,
>> 283751, 283251, 282751, 282251, 281751, 281251, 280751, 280251, 279751,
>> 279251, 278751, 278251, 277751, 277251, Error in qr.solve(t(TR) * wgths^2,
>> t(Genotypes) * wgths^2) :
>> singular matrix 'a' in solve
>>
>>
>> I tried a second run which leads to a similar error:
>> ...
>> 20180913 15:49:54| All data points are finite.
>> 20180913 15:49:54| Identifying non-finite data points...done
>> 20180913 15:49:54| Fitting CalMaTe...
>> 20180913 15:49:54| Algorithm flavor: v2
>> 20180913 15:49:54| Number of SNPs: 51525
>> 20180913 15:49:54| Number of SNPs left: 51525, 51025, 50525, 50025,
>> 49525, 49025, 48525, 48025, 47525, 47025, 46525, 46025, 45525, 45025, 44525,
>> 44025, 43525, 43025, 42525, 42025, 41525, 41025, 40525, 40025, 39525, 39025,
>> 38525, 38025, 37525, 37025, 36525, 36025, 35525, 35025, 34525, 34025, 33525,
>> 33025, 32525, 32025, 31525, 31025, 30525, 30025, 29525, 29025, 28525, 28025,
>> 27525, 27025, 26525, 26025, 25525, 25025, 24525, 24025, 23525, 23025, 22525,
>> 22025, 21525, 21025, 20525, 20025, 19525, Error in qr.solve(t(TR) * wgths^2,
>> t(Genotypes) * wgths^2) :
>> singular matrix 'a' in solve
>>
>>
>>
>>
>> And I get then the downstream error when I try to access the fitted
>> fractionB data:
>>
>> dsCTxt<- writeDataFrame(dsCList$fracB, columns=c("unitName", "chromosome",
>> "position", "*"))
>> Error in writeDataFrame(dsCList$fracB, columns = c("unitName", "chromosome",
>> : object 'dsCList' not found
>>
>>
>> Any suggestion how to find the cause of error and a resolution ?
>>
>>
>> > sessionInfo()
>> R version 3.5.1 (2018-07-02)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> Running under: Windows 7 x64 (build 7601) Service Pack 1
>>
>> Matrix products: default
>>
>> locale:
>> [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
>> LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
>> [5] LC_TIME=German_Germany.1252
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] calmate_0.12.1 aroma.light_3.10.0 aroma.affymetrix_3.1.1
>> aroma.core_3.1.3 R.devices_2.16.0
>> [6] R.filesets_2.12.1 R.utils_2.7.0 R.oo_1.22.0
>> affxparser_1.52.0 R.methodsS3_1.7.1
>>
>> loaded via a namespace (and not attached):
>> [1] matrixStats_0.54.0 codetools_0.2-15 listenv_0.7.0 future_1.9.0
>> digest_0.6.16 MASS_7.3-50R.huge_0.9.0
>> [8] future.apply_1.0.1 PSCBS_0.64.0 tools_3.5.1R.cache_0.13.0
>> parallel_3.5.1 compiler_3.5.1 base64enc_0.1-3
>> [15] aroma.apd_0.6.0R.rsp_0.43.0 globals_0.12.2 DNAcopy_1.54.0
>>
>>
>> best regards
>> Thomas
>>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.a
Re: [aroma.affymetrix] Error using RMA
Hi,
so that example code uses the affy package of Bioconductor and not the
aroma.affymetrix framework. It might be that there is a bug in the
affy package or that it does not support custom CDFs well enough. It
could also be that the chip type you're using is special and not well
suited from customization.
I would recommend you to make sure your custom CDF first using the
doRMA() function in aroma.affymetrix.
/Henrik
PS. Please do not hijack old email threads; instead start with a new
message whenever you have a new topic.
On Fri, Dec 22, 2017 at 8:32 AM, Pabita Saud wrote:
> Hi,
> I followed the aroma project to create a custom cdf package. I succeed in
> doing that. Now I want to see the expression of genes from a .cel file with
> my cdf package in compare to that with previous cdf. When I tried to use
> normalization (rma) to the affy object (with previous cdf), I can get
> expression set,
>
>>rawdata<-ReadAffy("GSM1090980_ZE010001.CEL",cdfname ="syng007a520046cdf" )
>
>>rawdata
> AffyBatch object
> size of arrays=1164x1164 features (17 kb)
> cdf=syng007a520046cdf (82661 affyids)
> number of samples=1
> number of genes=82661
> annotation=syng007a520046cdf
> notes=
>
>>rma(rawdata)
> Background correcting
> Normalizing
> Calculating Expression
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 82661 features, 1 samples
> element names: exprs
> protocolData
> sampleNames: GSM1090980_ZE010001.CEL
> varLabels: ScanDate
> varMetadata: labelDescription
> phenoData
> sampleNames: GSM1090980_ZE010001.CEL
> varLabels: sample
> varMetadata: labelDescription
> featureData: none
> experimentData: use 'experimentData(object)'
> Annotation: syng007a520046cdf
>
> But, if same process is applied to my cdf, I get an error,
>>rawdata_mycdf<-ReadAffy("GSM1090980_ZE010001.CEL",cdfname
>> ="gpl16720syng007a520046.mycdf")
>>rawdata_mycdf
> AffyBatch object
> size of arrays=1164x1164 features (17 kb)
> cdf=gpl16720syng007a520046.mycdf (8858 affyids)
> number of samples=1
> number of genes=8858
> annotation=gpl16720syng007a520046.mycdf
> notes=
>
>>rma(rawdata_mycdf)
> Error in exprs(object)[index, , drop = FALSE] : subscript out of bounds
>
> I will really appreciate your help.
> Thank you.
>
> Best Regards,
> Pabita
>
> Best Regards,
> Pabita
[...]
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
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>
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Re: [aroma.affymetrix] Error writing to connection
Hi. From your verbose output, I think two things can have happened:
1. This error happens when it tries to write to the file cache, which
is located under ~/.Rcache/. It could be that this cache is using up
your home drive/folder/account. Not sure what OS you're on, but to
find where `~` is use `normalizePath("~"). If that is indeed full,
and you're on Unix/macOS, the easiest is to simply point `~/.Rcache/`
to another drive via symbol links, e.g. `mkdir -p /scratch/$USER; mv
~/.Rcache /scratch/$USER/; ln -s /scratch/$USER/ ~/.Rcache`.
2. Alternatively, it could just be a hiccup on your system, which
means you can just rerun the script (it should quickly skip everything
already processed in previous runs).
I think (1) is the most likely reason, because the error is in
`base_save(file = fh, object, compress = compress, ...)` which happens
after two very similar calls to the same file which did _not_ fail,
cf. https://github.com/HenrikBengtsson/R.cache/blob/0.12.0/R/saveCache.R#L111.
(I'll see if I can add a more informative error message in a future
version of R.cache, e.g. including the problematic filename.)
Hope this helps
Henrik
On Mon, Dec 18, 2017 at 3:25 PM, Karyn Meltz Steinberg
wrote:
> Hello,
>
> I am running doCRMAv2 on 8 CytoScanHD .CEL files. I get the following error
> in the CRMAv2/Export to technology-independent data files...
> step:
>
> Error in base_save(file = fh, object, compress = compress, ...) :
> error writing to connection
> In addition: Warning message:
> In readRDS(con) : error reading from connection
> Saving to file cache...done
> Getting (unit, group, cell) map...done
> Extracting (total, freqB)...done
>Reading data...done
> Exporting CnChipEffectFile as an AromaUnitTotalCnBinaryFile...done
> Exporting (total, fracB) data...done
> Array #1 ('GBD-035') of 8...done
>Exporting CnChipEffectSet as AromaUnitTotalCnBinarySet...done
>
> I have enough space on the disk and the correct permissions. I am running
> version 3.1.0 on R3.4.0. Any advice would be greatly appreciated
>
> Best,
> Karyn
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
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>
> ---
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--
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version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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Re: [aroma.affymetrix] Error: object 'csC' not found.
If you called csC <- process(acc, verbose=verbose) and csC is not found, then there was an error during that call that you must pay attention to. /Henrik PS. Are you a single person reporting via three different email addresses, or are you two (three?) different people having the same problem? On Friday, November 24, 2017 at 12:18:31 PM UTC-8, 321bi...@gmail.com wrote: > > hello , i called the csC <- process(acc, verbose=verbose) and them > print(csC), it still met Error: object 'csC' not found. > 在 2017年11月24日星期五 UTC+8上午7:41:23，Henrik Bengtsson写道： >> >> Still the same; you're not calling >> >> csC <- process(acc, verbose=verbose) >> > -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] Error: object 'csC' not found.
Still the same; you're not calling csC <- process(acc, verbose=verbose) -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] CbsModel or writeRegions error
I've been trying to figure where the error could show up and I have
some "poor" guesses. In order to figure it out better, please install
the developer's version of R.utils, which I just updated:
source('http://callr.org/install#HenrikBengtsson/R.utils@develop')
If the error occurs anywhere related to the aroma framework or some of
my underlying packages, the error message should then be much more
informative - particularly, it'll show which the problematic file is.
Unfortunately, the above would require you to rerun your script (but
it should still skip already processed files). If it is the case that
one of the RDS files is corrupt, then a shortcut could be to do:
path <-
"cbsData/gdsc_all,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired/GenomeWideSNP_6/"
files <- dir(path = path, pattern = "*[.]rds$", full.names = TRUE)
for (file in files) {
message("Reading file: ", file)
res <- R.utils::loadObject(file)
}
That should identify the problematic file, iff such exists.
Without understanding the problem is and / or not having access to all
your *.rds files, it's hard to say if it's safe to export the segments
or not using writeRegions(), e.g. if there's one problematic file,
then it could be that you'll be missing all segments for that
particular sample and chromosome.
Hope this help
Henrik
On Thu, Aug 31, 2017 at 3:52 PM, Emanuel Gonçalves
wrote:
>> Hmm... assuming you're on a *nix-like system, see if there are any
>> empty (zero-size) RDS files is:
>>
>> ls -la
>> cbsData/gdsc_all,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired/GenomeWideSNP_6/*.rds
>>
>> The original error message suggests that there could exist such a file.
>
>
> Indeed, I was wondering about that. I only have *.xdr files, none had 0
> bites. Also there are 25 files per sample.
>
>> Also, you wrote "it systematically crashes on the last sample"; did
>> you run it multiple times and exact same error occurred at the exact
>> same place?
>
>
> Yes, I tried three times and always with the same error.
>
>> BTW, your mentioning 1020 samples, but the output says 1019 - probably
>> not important but better to make sure we're on the same page.
>
>
> In fact it's 1020 samples in total, but I excluded one sample when I got the
> first error (it was the very last sample). Then I re-run a sub-set of the
> last 20/30 samples containing the problematic ones, but I had no error and
> the regions were exported correctly.
>
>> The reason why I'm asking these questions, is to rule out
>> certain parts of the code. But, a traceback() would be the absolutely
>> most helpful information.
>
>
> I only had this error when running all the samples together in the
> CbsModel. Unfortunately, because it takes so long to load all the samples
> through CbsModel it's hard to debug. I'm running now the script with a
> try/catch.
>
> Is there an alternative way to export the regions without running the
> CbsModel again? I have the previous script running (where only the last
> sample was ran in CbsModel) and it seems to be exporting all the processed
> samples.
>
> Thanks a bunch,
>
>>
>>
>> /Henrik
>>
>> On Thu, Aug 31, 2017 at 2:42 PM, Emanuel Gonçalves
>> wrote:
>> > Hi Henrik,
>> >
>> >> does the error occur when you run:
>> >>
>> >> fit(cbs, verbose=verbose)
>> >
>> >
>> > Yes, because I never got the "print(cbs)" output
>> >
>> >>
>> >> or did that complete successfully and you get the error while running:
>> >>
>> >> pathname <- writeRegions(cbs, verbose=verbose)
>> >>
>> >> If you run interactively, what does traceback() output if called
>> >> immediately after the error occurs?
>> >
>> >
>> > Unfortunately, I can't run this interactively because even though the
>> > samples are already preprocessed it takes almost a day to load
>> > everything.
>> >
>> >> Also, see if
>> >>
>> >> fit(cbs, arrays = 1019:1020, chromosomes = c(1, 25), verbose = verbose)
>> >>
>> >> or alternatively,
>> >>
>> >> pathname <- writeRegions(cbs, arrays = 1019:1020, chromosomes = c(1,
>> >> 25), verbose=verbose)
>> >>
>> >> gives the same error.
>> >
>> >
>> > I changed the code accordingly:
>> >
>> > fit(cbs, arrays=1019:1020, chromosomes=c(1, 25), verbose=verbose)
>> >
>> > It ran without throwing any error (I tried before the same with a subset
>> > of
>> > ~100 samples and it also worked).
>> >
>> > It seems to be a specific problem when all the 1020 samples are ran
>> > together. I've placed a try/catch with the traceback().
>> >
>> > # Run CBS paired segmentation with pooled normal samples
>> > cbs <- CbsModel(cesN, cesN1.ref)
>> > out <- tryCatch(
>> > {
>> > fit(cbs, arrays=1019:1020, chromosomes=c(1, 25), verbose=verbose)
>> > },
>> > error=function() {
>> > message('Try/catch: error')
>> > traceback()
>> > },
>> > warning=function() {
>> > message('Try/catch: warning')
>> > traceback()
>> > },
>> > finally={
>> > message('Try/catch: finally')
>> > traceback()
>> > }
>> > )
>> > print(cbs)
>> >
>> > I started t
Re: [aroma.affymetrix] CbsModel or writeRegions error
Hmm... assuming you're on a *nix-like system, see if there are any
empty (zero-size) RDS files is:
ls -la
cbsData/gdsc_all,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired/GenomeWideSNP_6/*.rds
The original error message suggests that there could exist such a file.
Also, you wrote "it systematically crashes on the last sample"; did
you run it multiple times and exact same error occurred at the exact
same place? The reason why I'm asking these questions, is to rule out
certain parts of the code. But, a traceback() would be the absolutely
most helpful information.
BTW, your mentioning 1020 samples, but the output says 1019 - probably
not important but better to make sure we're on the same page.
/Henrik
On Thu, Aug 31, 2017 at 2:42 PM, Emanuel Gonçalves
wrote:
> Hi Henrik,
>
>> does the error occur when you run:
>>
>> fit(cbs, verbose=verbose)
>
>
> Yes, because I never got the "print(cbs)" output
>
>>
>> or did that complete successfully and you get the error while running:
>>
>> pathname <- writeRegions(cbs, verbose=verbose)
>>
>> If you run interactively, what does traceback() output if called
>> immediately after the error occurs?
>
>
> Unfortunately, I can't run this interactively because even though the
> samples are already preprocessed it takes almost a day to load everything.
>
>> Also, see if
>>
>> fit(cbs, arrays = 1019:1020, chromosomes = c(1, 25), verbose = verbose)
>>
>> or alternatively,
>>
>> pathname <- writeRegions(cbs, arrays = 1019:1020, chromosomes = c(1,
>> 25), verbose=verbose)
>>
>> gives the same error.
>
>
> I changed the code accordingly:
>
> fit(cbs, arrays=1019:1020, chromosomes=c(1, 25), verbose=verbose)
>
> It ran without throwing any error (I tried before the same with a subset of
> ~100 samples and it also worked).
>
> It seems to be a specific problem when all the 1020 samples are ran
> together. I've placed a try/catch with the traceback().
>
> # Run CBS paired segmentation with pooled normal samples
> cbs <- CbsModel(cesN, cesN1.ref)
> out <- tryCatch(
> {
> fit(cbs, arrays=1019:1020, chromosomes=c(1, 25), verbose=verbose)
> },
> error=function() {
> message('Try/catch: error')
> traceback()
> },
> warning=function() {
> message('Try/catch: warning')
> traceback()
> },
> finally={
> message('Try/catch: finally')
> traceback()
> }
> )
> print(cbs)
>
> I started the script with all the samples (without "arrays=1019:1020") as
> before.
>
> What surprised me is that the script continued to the writeRegions call and
> it started to export all the samples.
>
> pathname <- writeRegions(cbs, verbose=verbose)
>
>> > # Export CBS regions
>> > pathname <- writeRegions(cbs, verbose=verbose)
>> 20170831 21:53:10|Array #1 ('201T') of 1019...
>> 20170831 21:53:10| Extracting regions from all fits...
>> 20170831 21:53:10| Obtaining CN model fits (or fit if missing)...
>> 20170831 21:57:15| Obtaining CN model fits (or fit if missing)...done
>> 20170831 21:57:15| Extracting regions for chromosome #1...
>> 20170831 21:57:15| Extracting regions for chromosome #1...done
>> 20170831 21:57:15| Extracting regions for chromosome #2...
>> 20170831 21:57:15| Extracting regions for chromosome #2...done
>> 20170831 21:57:15| Extracting regions for chromosome #3...
>> 20170831 21:57:15| Extracting regions for chromosome #3...done
>
>
> Does it mean it will export all the samples processed so far? Can I export
> everything without re-calling the fit function from CbsModel?
>
> Thanks a lot,
>
>>
>> Then you can get to traceback() a bit sooner.
>>
>> /Henrik
>>
>> PS. I assume that you already know that rerunning the commands will
>> not redo the actual analysis; already processed samples will be
>> skipped - though with 1020 samples it might still take some time.
>>
>>
>> On Thu, Aug 31, 2017 at 1:26 AM, Emanuel Gonçalves
>> wrote:
>> > Hi all,
>> >
>> > I'm processing a large set of SNP6 samples (1020) and performing CBS
>> > segmentations afterwards. It's a very lengthy process and the annoying
>> > part
>> > is that it systematically crashes on the last sample, see code and
>> > output
>> > below:
>> >
>> > # Run CBS paired segmentation with pooled normal samples
>> > cbs <- CbsModel(cesN, cesN1.ref)
>> > fit(cbs, verbose=verbose)
>> > print(cbs)
>> >
>> > # Export CBS regions
>> > pathname <- writeRegions(cbs, verbose=verbose)
>> >
>> >
>> >> 20170831 06:57:51| Pathname:
>> >>
>> >> cbsData/gdsc_all,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired/GenomeWideSNP_6/YKG-1,chr25,6c653767ed90d29ad5254a760d8f3952.xdr
>> >> 20170831 06:57:51| Already done. Skipping.
>> >> 20170831 06:57:51|Array #1018 ('YKG-1') of 1019 on chromosome 25...done
>> >> 20170831 07:01:07|Genomic-signal tags:
>> >> 20170831 07:01:07|Reference tags: 6c653767ed90d29ad5254a760d8f3952
>> >> 20170831 07:01:08|Array #1019 ('YMB-1-E') of 1019 on chromosome 1...
>> >> 20170831 07:01:08| Pathname:
>> >>
>> >> cbsData/gdsc_all,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired/GenomeWideSNP_6/Y
Re: [aroma.affymetrix] CbsModel or writeRegions error
Hi,
does the error occur when you run:
fit(cbs, verbose=verbose)
or did that complete successfully and you get the error while running:
pathname <- writeRegions(cbs, verbose=verbose)
If you run interactively, what does traceback() output if called
immediately after the error occurs?
Also, see if
fit(cbs, arrays = 1019:1020, chromosomes = c(1, 25), verbose = verbose)
or alternatively,
pathname <- writeRegions(cbs, arrays = 1019:1020, chromosomes = c(1,
25), verbose=verbose)
gives the same error. Then you can get to traceback() a bit sooner.
/Henrik
PS. I assume that you already know that rerunning the commands will
not redo the actual analysis; already processed samples will be
skipped - though with 1020 samples it might still take some time.
On Thu, Aug 31, 2017 at 1:26 AM, Emanuel Gonçalves
wrote:
> Hi all,
>
> I'm processing a large set of SNP6 samples (1020) and performing CBS
> segmentations afterwards. It's a very lengthy process and the annoying part
> is that it systematically crashes on the last sample, see code and output
> below:
>
> # Run CBS paired segmentation with pooled normal samples
> cbs <- CbsModel(cesN, cesN1.ref)
> fit(cbs, verbose=verbose)
> print(cbs)
>
> # Export CBS regions
> pathname <- writeRegions(cbs, verbose=verbose)
>
>
>> 20170831 06:57:51| Pathname:
>> cbsData/gdsc_all,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired/GenomeWideSNP_6/YKG-1,chr25,6c653767ed90d29ad5254a760d8f3952.xdr
>> 20170831 06:57:51| Already done. Skipping.
>> 20170831 06:57:51|Array #1018 ('YKG-1') of 1019 on chromosome 25...done
>> 20170831 07:01:07|Genomic-signal tags:
>> 20170831 07:01:07|Reference tags: 6c653767ed90d29ad5254a760d8f3952
>> 20170831 07:01:08|Array #1019 ('YMB-1-E') of 1019 on chromosome 1...
>> 20170831 07:01:08| Pathname:
>> cbsData/gdsc_all,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired/GenomeWideSNP_6/YMB-1-E,chr01,6c653767ed90d29ad5254a760d8f3952.xdr
>> 20170831 07:01:08| Already done. Skipping.
>> Error: empty (zero-byte) input file
>> Execution halted
>
>
> At first I thought it was a problem of the sample, but that is not the case
> as I could process it separately. In fact, at this stage all the samples
> seem to be processed. Also strange is that the script works and exports the
> regions for subsets of the data-set.
>
> Any suggestion in how to export these would be much appreciated?
>
> Thank you,
>
> P.S: I'm using the multithreaded option of aroma
>
> # - Setup configurations
> # options(mc.cores = 10)
> print(future::availableCores())
>
> # Multithreaded
> future::plan('multiprocess')
>
> # Increase ram
> setOption(aromaSettings, 'memory/ram', 600.0)
>
> # Logs
> log <- verbose <- Arguments$getVerbose(-4, timestamp=TRUE)
>
> # Reduce decimal places to minimize space
> options(digits=4)
>
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> ---
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Re: [aroma.affymetrix] CBS input dataframe
Ah, my bad - you're correct.
On Tue, Jun 20, 2017 at 4:40 PM, Emanuel Gonçalves
wrote:
> I think what I'm looking for is:
>
>> extractRawCopyNumbers(cbsmodel, array=1, chromosome=2)
>
>
> Problem is I have ~200 and the function seems to be taking quite sometime to
> get me the results (is this because I don't have all the cbs computed yet?),
> is there a way to export the whole data-set raw copy numbers?
Yes, that's the way to do it.
That's what fit() for CbsModel is using internally, and yes, there's a
bit of overhead in each of those calls. There's quite a bit of
validation etc going on. It's probably possible to make it faster for
the case when one would want to pull out data for all samples and all
chromsomes at once - but, as far as I remember, I don't think we
implemented that per se. If you want to do your own segmentation, see
example at the end.
These day you can parallelize it quite easily using future, cf.
http://www.aroma-project.org/howtos/parallel_processing/. For
example, here's how you can extract chromosomes in parallel:
future::plan("multiprocess")
array <- 1L
cns <- future_lapply(1:23, FUN = function(chr) {
extractRawCopyNumbers(cbsmodel, array = array, chromosome = chr)
})
If you have completed fit(), then all the CBS results (segments and
locus-level data) are saved to file for each (array, chromosome).
These "internal" data files are located in:
path <- getPath(sm)
You can pull out, say, all Chr 1 results across all samples as:
pathnames <- dir(path = getPath(sm), pattern = ",chr01,", full.names = TRUE)
fits <- lapply(pathnames, FUN = loadObject)
locusData <- lapply(fits, FUN = `[[`, "data")
However, those files don't contain information of the cell names
("clones" aka "probe names").
Below is a way you can get the normalized locus-level CN signals that
can be used for downstream segmentation. This example uses
Mapping10K_Xba142 data, but the idea is the same:
> clones <- getUnitNames(getUnitNamesFile(gsT))
> positions <- readDataFrame(getAromaUgpFile(gsT))
> signals <- extractMatrix(gsT)
> data <- cbind(clones, positions, signals)
> str(data)
'data.frame': 10208 obs. of 13 variables:
$ clones: Factor w/ 10208 levels "AFFX-5Q-123",..: 1 2 3 4 5013
9020 3048 8172 4263 10008 ...
$ chromosome: int NA NA NA NA 6 7 10 1 15 12 ...
$ position : int NA NA NA NA 162491313 42608794 68113302 22754354
28848178 53641300 ...
$ GSM226867 : num 5209 2042 5005 3750 1563 ...
$ GSM226868 : num 4799 1995 4726 3719 1675 ...
$ GSM226869 : num 5069 2070 4661 3450 1881 ...
$ GSM226870 : num 5502 2492 5164 3809 1828 ...
$ GSM226871 : num 5462 2298 4917 3678 2131 ...
$ GSM226872 : num 5232 1886 4671 3459 2227 ...
$ GSM226873 : num 5878 2479 5588 4372 1817 ...
$ GSM226874 : num 6363 2668 5768 4356 1396 ...
$ GSM226875 : num 4789 1765 4543 3610 1876 ...
$ GSM226876 : num 4762 1876 4614 3241 2568 ...
With those data, you can run your own segmentation - but you do have
to worry about how calculate CN ratios, i.e. what is T and what is N
in C = T / N etc.
Hope this helps
Henrik
>
> Thank you,
>
> On Tuesday, June 20, 2017 at 10:33:36 PM UTC+1, Emanuel Gonçalves wrote:
>>
>> Hi Henrik,
>>
>>> There's no direct way of doing this, but as a start you can read in
>>> all the writeRegions()-exported segment data for all samples in a data
>>> set as explained in
>>> http://www.aroma-project.org/vignettes/NonPairedCBS/. That will give
>>> you a data.frame.
>>
>>
>> But that would get me the segmentation regions, right? What I want is to
>> export the input of CBS.
>>
>>> > # -- SNP6 cancer cell lines preprocessing with CRMA (v2)
>>> > gsT <- doCRMAv2("cancer_lines", chipType="GenomeWideSNP_6,Full",
>>> > verbose=verbose)
>>> > print('cancer_lines CRMAv2 done.')
>>
>>
>> In other words, is there a writeRegions function for "gsT" to export it as
>> a table with the probe, chromosome, position and the ratios per sample.
>>
>> Thank you for your time,
>>
>>> >
>>> > # -- Segmentation (CBS)
>>> > sm <- CbsModel(gsT)
>>> > fit(sm, verbose=verbose)
>>> > print('CbsModel done.')
>>> >
>>> > # -- Export segmentation
>>> > pathname <- writeRegions(sm, verbose=verbose)
>>> > print('Exported done.')
>>> >
>>> > I would like to extract the gsT as a data.frame in the format that is
>>> > used
>>> > in DNAcopy:
>>> >
>>> >> library(DNAcopy)
>>> >> data(coriell)
>>> >> head(coriell)
>>> > Clone Chromosome Position Coriell.05296 Coriell.13330
>>> > 1 GS1-232B23 10NA 0.207470
>>> > 2 RP11-82d16 1 468 0.008824 0.063076
>>> > 3 RP11-62m23 1 2241 -0.000890 0.123881
>>> > 4 RP11-60j11 1 4504 0.075875 0.154343
>>> > 5 RP11-111O05 1 5440 0.017303 -0.043890
>>> > 6 RP11-51b04 1 7000 -0.006770 0.094144
>>> >
>>> > Thank you in advance,
>>> >
>>> > --
>>> > --
>>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>
Re: [aroma.affymetrix] CBS input dataframe
Hi.
There's no direct way of doing this, but as a start you can read in
all the writeRegions()-exported segment data for all samples in a data
set as explained in
http://www.aroma-project.org/vignettes/NonPairedCBS/. That will give
you a data.frame.
>From there you should be able to manipulate the content of the
data.frame using basic R tools, e.g. subset(), rbind(), cbind() etc.
The dplyr package might be a more convenient way of doing it - it's
the ninja-tool for data.frame manipulations.
Hope this help
Henrik
PS. Feel free to share your solution here.
On Tue, Jun 20, 2017 at 10:04 AM, Emanuel Gonçalves
wrote:
> Dear all,
>
> I'm processing a set of ~200 SNP6 .cel files and then performing
> segmentation with CBS. But I would like to know how to extract the data
> points data-frame that is used as input to DNAcopy CBS.
>
> The code is as below:
>
> # install.packages('aroma.affymetrix', repos='http://cran.us.r-project.org')
> library("aroma.affymetrix")
>
> # Logs
> log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>
> # Reduce decimal places to minimize space
> options(digits=4)
> print('Options configured')
>
> # -- SNP6 cancer cell lines preprocessing with CRMA (v2)
> gsT <- doCRMAv2("cancer_lines", chipType="GenomeWideSNP_6,Full",
> verbose=verbose)
> print('cancer_lines CRMAv2 done.')
>
> # -- Segmentation (CBS)
> sm <- CbsModel(gsT)
> fit(sm, verbose=verbose)
> print('CbsModel done.')
>
> # -- Export segmentation
> pathname <- writeRegions(sm, verbose=verbose)
> print('Exported done.')
>
> I would like to extract the gsT as a data.frame in the format that is used
> in DNAcopy:
>
>> library(DNAcopy)
>> data(coriell)
>> head(coriell)
> Clone Chromosome Position Coriell.05296 Coriell.13330
> 1 GS1-232B23 10NA 0.207470
> 2 RP11-82d16 1 468 0.008824 0.063076
> 3 RP11-62m23 1 2241 -0.000890 0.123881
> 4 RP11-60j11 1 4504 0.075875 0.154343
> 5 RP11-111O05 1 5440 0.017303 -0.043890
> 6 RP11-51b04 1 7000 -0.006770 0.094144
>
> Thank you in advance,
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
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>
> ---
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[aroma.affymetrix] aroma.affymetrix 3.1.0 release
aroma.affymetrix 3.1.0 and friends have been updated and are being
rolled out on CRAN. These days I mostly do maintenance, fix bugs,
refactor code, and optimize the performance of these packages. As
usual, all released undergo rigorous validation based on system tests
running for ~50 CPU hours (so a lot of tests).
For full update details, see the end of this message. To update, just
do update.packages() or:
source("http://callr.org/install#aroma.affymetrix";)
Also, don't forget that it's extremely simple to process samples in
parallel (when the algorithm allows). For instance, call:
library("future")
plan(multiprocess)
before starting your analysis and the samples will run in parallel on
your local machine. If you call,
library("future.BatchJobs")
plan(batchjobs_torque)
then the samples will be processed in parallel via the TORQUE / PBS
scheduler on your HPC cluster (if you have one). See
http://aroma-project.org/howtos/parallel_processing/ for other
alternatives.
Cheers,
Henrik
(http://www.aroma-project.org/)
Details on updated since aroma.affymetrix 3.0.0 (2016-01-09).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Updates to aroma.affymetrix
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Version: 3.1.0 [2017-03-23]
NEW FEATURES:
o Now file and object sizes are reported using IEC binary prefixes,
i.e. bytes, KiB, MiB, GiB, TiB, ..., YiB.
o Now doNnn() methods can be called directly from the command line, e.g.
Rscript -e aroma.affymetrix::doCRMAv2 --dataSet=HapMap270
--chipType=GenomeWideSNP_6
o Objects no longer report on memory (RAM) usage.
REFACTORIZATION:
o Used partial element name 'coef' instead of 'coefficients' for lm() fit.
BUG FIXES:
o Package used %<=% internally with was deprecated in future (>= 1.4.0).
o ROBUSTNESS: Some regular expression patterns used for locating files
would match any symbol when it intended to match only a period.
o The International HapMap Project (http://www.hapmap.org/) is being retired
and HTTP server http://hapmap.ncbi.nlm.nih.gov/downloads/raw_data/ is
decomissioned. System test scripts updated to download HapMap CEL files
from the FTP server ftp://ftp.ncbi.nlm.nih.gov/hapmap/raw_data/ instead.
DEPRECATED AND DEFUNCT:
o Methods bgAdjustRma(), bgAdjustOptical() and bgAdjustGcrma() for
AffymetrixCelFile as well as bgAdjustGcrma() for AffymetrixCelSet
are now defunct.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Updates to aroma.core
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Version: 3.1.0 [2017-03-22]
NEW FEATURES:
o Now file sizes are reported using IEC binary prefixes, i.e. bytes, KiB,
MiB, GiB, TiB, ..., YiB.
o Now genomic positions / distances are reported in 'Mbp' (was 'MB' and 'Mb').
o Objects no longer report on memory (RAM) usage.
BUG FIXES:
o Package used %<=% internally with was deprecated in future (>= 1.4.0).
o exportTotalCnRatioSet() for AromaUnitTotalCnBinarySet and
exportFracBDiffSet() for AromaUnitFracBCnBinarySet would return files with
file names matching `.asb`, which would incorrectly also include `.asb.md5`
files. Thanks to Thomas Grombacher at the Merck Group for the report.
DEPRECATED AND DEFUNCT:
o Default method whatDataType() is now defunct.
o Argument '.old' of getChipType() for AromaMicroarrayTabularBinaryFile is
now defunct (was deprecated in 2008!).
o Previously deprecated argument 'maxNAFraction' to getRawCnData() of
CopyNumberChromosomalModel and for fit() of CopyNumberSegmentationModel
is now defunct.
o Removed previously defunct apply() for SampleAnnotationFile.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Updates to R.filesets
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Version: 2.11.0 [2017-02-27]
SIGNIFICANT CHANGES:
o Package requires R (>= 3.1.2) and BioC (>= 3.0) both released in
October 2014.
NEW FEATURES:
o Now getChecksum() for ChecksumFile defaults to not creating a checksum file
(which is the default for other types of file), but instead always return
the checksum of the file by only calculating and in memory. This prevents
for instance the equals() test on two different checksum files to generate
another set of checksum files on themselves.
o Now findByName() for GenericDataFileSet reports on the non-existing
root paths in error messages.
o GenericDataFile and GenericDataFileSet no longer report on memory (RAM)
usage of objects.
CLEANUP:
o dsApply(..., .parallel="future") now used future_lapply() of the future
package internally. dsApply() will soon be deprecated (see below).
INSTALLATION:
o Package no longer needs to depend on listenv.
DEPRECATED AND DEFUNCT:
o Argument 'colClassPatterns' of readDataFrame() for TabularTextFile is
now defunct. Use 'colClasses' instead.
o Argument 'files' of extractMatrix()
Re: [aroma.affymetrix] troubles in doing PCR fragment length normalization AROMA3.0
>ok <- rho <- NULL
>verbose && cat(verbose, "Normalized thetas:")
>verbose && str(verbose, theta)
>verbose && summary(verbose, theta)
>verbose && exit(verbose)
>verbose && enter(verbose, "Creating CEL file for results, if missing")
>isFile <- isFile(pathname)
>pathnameT <- pushTemporaryFile(pathname, isFile = isFile,
>verbose = verbose)
>ceN <- createFrom(ce, filename = pathnameT, path = NULL,
>verbose = less(verbose))
>verbose && exit(verbose)
>if (inherits(ce, "SnpChipEffectFile")) {
>ceN$mergeStrands <- ce$mergeStrands
>if (inherits(ce, "CnChipEffectFile")) {
>ceN$combineAlleles <- ce$combineAlleles
>}
>}
>setCdf(ceN, cdf)
>verbose && enter(verbose, "Storing normalized signals")
>ok <- which(is.finite(cellMatrixMap))
>cells <- cellMatrixMap[ok]
>data <- theta[ok]
>ok <- theta <- NULL
>verbose2 <- -as.integer(verbose) - 5
>pathnameN <- getPathname(ceN)
>.updateCel(pathnameN, indices = cells, intensities = data,
>verbose = verbose2)
>cells <- data <- ceN <- NULL
>verbose && exit(verbose)
>popTemporaryFile(pathnameT, verbose = verbose)
>dfZ <- getChecksumFile(pathname)
>gc <- gc()
>verbose && print(verbose, gc)
>pathname
>}
> 2: process.FragmentLengthNormalization(fln, verbose = verbose)
> 1: process(fln, verbose = verbose)
>
> -Ursprüngliche Nachricht-
> Von: aroma-affymetrix@googlegroups.com
> [mailto:aroma-affymetrix@googlegroups.com] Im Auftrag von Henrik Bengtsson
> Gesendet: Mittwoch, 13. Juli 2016 17:45
> An: aroma-affymetrix
> Betreff: Re: [aroma.affymetrix] troubles in doing PCR fragment length
> normalization AROMA3.0
>
> That looks like a hiccup in the file system or something. Did you try again?
>
> Also, if the error remains, please report what traceback() outputs (as the
> first command after you get the error).
>
> /Henrik
>
> On Wed, Jul 13, 2016 at 4:19 AM, wrote:
>> Hello,
>>
>> I have used the standard pipeline for SNP6 CEL files described in the
>> CRMAv2 vignette. I did run the pipeline before several times, without any
>> issue.
>> Now, the fragment length normalization step failed with an error:
>>
>> Error in gzfile(file, mode) : cannot open the connection
>>
>> I am not clear where this error comes from.
>> Any support or idea is welcome.
>>
>> Best regards,
>> Thomas
>>
>> My sessionInfo:
>>
>>> sessionInfo()
>>
>> R version 3.2.1 (2015-06-18)
>>
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>>
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>>
>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>>
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>>
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>>
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>>
>> [1] aroma.light_3.0.0 aroma.affymetrix_3.0.0 aroma.core_3.0.0
>>
>> [4] R.devices_2.14.0 R.filesets_2.10.0 R.utils_2.3.0
>>
>> [7] R.oo_1.20.0 affxparser_1.42.0 R.methodsS3_1.7.1
>>
>> loaded via a namespace (and not attached):
>>
>> [1] matrixStats_0.50.2 codetools_0.2-14 listenv_0.6.0 future_0.14.0
>>
>> [5] digest_0.6.9 R.huge_0.9.0 PSCBS_0.61.0 tools_3.2.1
>>
>> [9] R.cache_0.12.0 parallel_3.2.1 base64enc_0.1-3 aroma.apd_0.6.0
>>
>> [13] R.rsp_0.30.0 globals_0.6.1 DNAcopy_1.44.0
>>
>>
>> The full output of the process(fln, verbose=verbose) function:
>>
>>> cesN <- process(fln, verbose=verbose)
>>
>>
>> 20160713 12:50:05|Normalizing set for PCR fragment-length effects...
>>
>>
>> 20160713 12:51:07| Identifying SNP and CN units...
>>
>>
>> types
>>
>>
>> 1 2 5
>>
>>
>> 621 934968 945826
>>
>>
>> 20160713 12:51:09| subsetToUpdate:
>>
>>
>> int [1:1880794] 622 623 624 625 626 627 628 629 630 631 ...
>>
>>
>> 20160713 12:51:09| Identifying SNP and CN units...done
>>
>>
&
Re: [aroma.affymetrix] Error while setting up AffymetrixCelSet
Hmm... this looks weird but as usual, there's probably a simple
explanation to it. Yes, it could possibly be that the CDF is
incompatible with the CEL files, but in that case I'd expect an
informative error message explaining why.
In a fresh R session, what does the following output?
library("aroma.affymetrix")
cdf <- AffymetrixCdfFile$byChipType("hjay", tags="r1,TC")
cs <- AffymetrixCelSet$byName("Data_Study1", cdf=cdf, verbose=-100)
The output is quite long, but it'll help me/you troubleshoot.
Also, what's the output of sessionInfo() after the above?
/Henrik
On Mon, Aug 1, 2016 at 1:17 PM, Marijke VAN MOERBEKE
wrote:
> Dear all
>
> I run into an error while setting up a CELset with my data. I've checked the
> structure of the folder annotationData and rawData and this is as
> instructed. My working directory contains the folders annotationData and
> rawData which both have a folder "hjay" (my chiptype) containing the cdf and
> CEL files respectively. My code is as follows:
>
> library(aroma.affymetrix)
>
> chipType<-"hjay"
> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="r1,TC")
> print(cdf)
> # AffymetrixCdfFile:
> # Path: annotationData/chipTypes/hjay
> # Filename: hjay,r1,TC.cdf
> # File size: 103.36 MiB (108385660 bytes)
> # Chip type: hjay,r1,TC
> # RAM: 0.00MB
> # File format: v4 (binary; XDA)
> # Dimension: 2558x2560
> # Number of cells: 6548480
> # Number of units: 33516
> # Cells per unit: 195.38
> # Number of QC units: 0
>
> cs <- AffymetrixCelSet$byName("Data_Study1",cdf=cdf,verbose=TRUE);
> #which runs into the following error
>
> Exception: Failed to setup a data set for any of 1 data directories located.
> The following reasons were reported: (1) Failed to create AffymetrixCdfFile
> object. Could not locate an annotation data file for chip type 'hjay'
> (without requiring any tags) and with filename extension 'cdf'. (while
> trying './rawData/Data_Study1/hjay').
>
> at #03. byName.AffymetrixCelSet(static, ...)
> - byName.AffymetrixCelSet() is in environment 'aroma.affymetrix'
>
> at #02. byName(static, ...)
> - byName() is in environment 'R.filesets'
> - originating from ''
>
> at #01. AffymetrixCelSet$byName("HTA_RASA", cdf = cdf, verbose = TRUE)
> - AffymetrixCelSet$byName() is local of the calling function
>
> Error: Failed to setup a data set for any of 1 data directories located. The
> following reasons were reported: (1) Failed to create AffymetrixCdfFile
> object. Could not locate an annotation data file for chip type 'hjay'
> (without requiring any tags) and with filename extension 'cdf'. (while
> trying './rawData/HTA_RASA/hjay').
>
> I created the cdf file myself. Is it possible that that I made a mistake
> during this process that can already be detected by AffymetrixCelSet$byName?
>
> Thank you for any help!
>
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> ---
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--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
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To unsubscribe and other options, go to http://www.aroma-project.org/forum/
---
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To unsubscribe from this group and stop receiving emails from it, send an email
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Re: [aroma.affymetrix] troubles in doing PCR fragment length normalization AROMA3.0
That looks like a hiccup in the file system or something. Did you try again? Also, if the error remains, please report what traceback() outputs (as the first command after you get the error). /Henrik On Wed, Jul 13, 2016 at 4:19 AM, wrote: > Hello, > > I have used the standard pipeline for SNP6 CEL files described in the CRMAv2 > vignette. I did run the pipeline before several times, without any issue. > Now, the fragment length normalization step failed with an error: > > Error in gzfile(file, mode) : cannot open the connection > > I am not clear where this error comes from. > Any support or idea is welcome. > > Best regards, > Thomas > > My sessionInfo: > >> sessionInfo() > > R version 3.2.1 (2015-06-18) > > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > > [1] aroma.light_3.0.0 aroma.affymetrix_3.0.0 aroma.core_3.0.0 > > [4] R.devices_2.14.0 R.filesets_2.10.0 R.utils_2.3.0 > > [7] R.oo_1.20.0 affxparser_1.42.0 R.methodsS3_1.7.1 > > loaded via a namespace (and not attached): > > [1] matrixStats_0.50.2 codetools_0.2-14 listenv_0.6.0 future_0.14.0 > > [5] digest_0.6.9 R.huge_0.9.0 PSCBS_0.61.0 tools_3.2.1 > > [9] R.cache_0.12.0 parallel_3.2.1 base64enc_0.1-3 aroma.apd_0.6.0 > > [13] R.rsp_0.30.0 globals_0.6.1 DNAcopy_1.44.0 > > > The full output of the process(fln, verbose=verbose) function: > >> cesN <- process(fln, verbose=verbose) > > > 20160713 12:50:05|Normalizing set for PCR fragment-length effects... > > > 20160713 12:51:07| Identifying SNP and CN units... > > > types > > > 1 2 5 > > > 621 934968 945826 > > > 20160713 12:51:09| subsetToUpdate: > > > int [1:1880794] 622 623 624 625 626 627 628 629 630 631 ... > > > 20160713 12:51:09| Identifying SNP and CN units...done > > > 20160713 12:51:09| Retrieving SNP information annotations... > > > UflSnpInformation: > > > Name: GenomeWideSNP_6 > > > Tags: Full,na33,hg19,dbSNP137,HB20140118 > > > Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118 > > > Pathname: > annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118.ufl > > > File size: 7.18 MiB (7526422 bytes) > > > RAM: 0.00 MB > > > Chip type: GenomeWideSNP_6,Full > > > Number of enzymes: 2 > > > 20160713 12:51:10| Retrieving SNP information annotations...done > > > 20160713 12:51:10| Identifying the subset used to fit normalization > function(s)... > > > 20160713 12:51:10| Identifying units that are SNP and CN probes... > > > UflSnpInformation: > > > Name: GenomeWideSNP_6 > > > Tags: Full,na33,hg19,dbSNP137,HB20140118 > > > Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118 > > > Pathname: > annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118.ufl > > > File size: 7.18 MiB (7526422 bytes) > > > RAM: 0.00 MB > > > Chip type: GenomeWideSNP_6,Full > > > Number of enzymes: 2 > > > 20160713 12:51:10| Identifying SNPs and CN probes... > > > types > > > 1 2 5 > > > 621 934968 945826 > > > 20160713 12:51:11| units: > > > int [1:1880794] 622 623 624 625 626 627 628 629 630 631 ... > > > 20160713 12:51:11| Identifying SNPs and CN probes...done > > > 20160713 12:51:11| Identify subset of units from genome information... > > > 20160713 12:51:11| subsetToFit: -XY > > > UgpGenomeInformation: > > > Name: GenomeWideSNP_6 > > > Tags: Full,na33,hg19,dbSNP137,HB20140118 > > > Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118 > > > Pathname: > annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118.ugp > > > File size: 8.97 MiB (9407882 bytes) > > > RAM: 0.00 MB > > > Chip type: GenomeWideSNP_6,Full > > > 20160713 12:51:18| Units to exclude: > > > int [1:96544] 61101 61102 61103 61104 61105 61106 61107 61108 61109 61110 > ... > > > 20160713 12:51:19| Units to include: > > > int [1:1784871] 1 2 3 4 5 6 7 8 9 10 ... > > > 20160713 12:51:19| Identify subset of units from genome information...done > > > 20160713 12:51:19| Reading fragment lengths... > > > 20160713 12:51:19| Reading and filtering fragment lengths... > > > 20160713 12:51:19| Reading fragment lengths... > > > UflSnpInformation: > > > Name: GenomeWideSNP_6 > > > Tags: Full,na33,hg19,dbSNP137,HB20140118 > > > Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118 > > > Pathname: > annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118.ufl > > > File size: 7.18 MiB (7526422 bytes) > > > RAM: 0.00 MB > > > Chip type: GenomeWideSNP_6,Full > > > Number of enzymes: 2 > > > 20160713 12:51:26| Summary of non-filtered fragment lengths: > > > int [1:1880794, 1:2] 395 4056 633 831
Re: [aroma.affymetrix] CytoScanHD_Array: problems with CbsModel(), 'Failed to locate Class object for class 'FutureError'
Hi.
On Mon, Jul 4, 2016 at 12:43 AM, roman.hillje via aroma.affymetrix
wrote:
> Hey Henrik, first of all thanks for the effort and your help! As you
> suggested, I installed the 'fixed' future package and set future::plan to
> 'eager' and now receive the following message upon fit(cbs):
>
> Error: Something is wrong with the copy-number ratios of sample
> 'GSM1704973,chipEffects' relative to reference
> '.baseline,aa03679a3cdfd0f39ecaf0c9a2c80eeb' on chromosome 1. Too many
> non-finite values: 231306 (100.0% > 20.0%) out of 231306. If this is
> expected, you may adjust argument 'maxNAFraction' when setting up
> CbsModel().
Good to see that the new future no longer hides this true error
message. FYI, future 1.0.1 is now on CRAN, so a regular
update.packages() should give you that.
>
>
> So, all CN ratios are NA, right? If so, I guess the problem is upstream,
> perhaps in one of the normalization steps?
If either the tumor or the normal (or pooled reference) is very noisy,
the above sanity check may trigger an error. However, in those cases,
you wouldn't expect all signals to be non-finite (i.e. all missing).
So it is not obvious to me what's wrong. There could be many reasons
for this. Have a look at the signals from your tumor and your pooled
normal to see if they make sense. I suspect one of them have failed,
either as a bad hyrbidization / array or an incomplete write in the
preprocessing (although I don't see how that should happen because
everything is written atomically). If other tumor vs pooled normals
work, then it is most likely a problem with the tumor sample and not
the pooled normals.
Hope this helps
Henrik
>
> On Saturday, July 2, 2016 at 4:46:26 AM UTC+2, Henrik Bengtsson wrote:
>>
>> Also, install the following version of the future package:
>>
>>
>> source("http://callr.org/install#HenrikBengtsson/future@FutureErrorFix";)
>>
>> This should reveal the true underlying error message.
>>
>> /Henrik
>>
>> On Friday, July 1, 2016 at 11:09:36 AM UTC-7, Henrik Bengtsson wrote:
>>>
>>> Unfortunately, there's a "bug" in future 1.0.0 causing the actual
>>> error to be disguised as "Cannot get static instance. ..."; there
>>> should really be an informative error message, cf.
>>> https://github.com/HenrikBengtsson/future/issues/83.
>>>
>>> But your traceback gives some more information and I see you're using
>>> parallel processing, i.e. you're using:
>>>
>>> plan(multiprocess)
>>>
>>> somewhere at the beginning of your script, correct? As a starter,
>>> could you retry with:
>>>
>>> plan(eager)
>>>
>>> If that works / doesn't work, at least it'll give some more clues
>>> what's going on.
>>>
>>> In the meanwhile, I'll try to fix that future bug causing us not to
>>> see the actual error message. When I've got a working fix, I'll share
>>> a early-access version with you.
>>>
>>> /Henrik
>>>
>>>
>>>
>>> On Fri, Jul 1, 2016 at 8:02 AM, roman.hillje via aroma.affymetrix
>>> wrote:
>>> > Thanks for the comment. Unfortunately, the error persists even after
>>> > the
>>> > updates. Here is the sessionInfo() output:
>>> >
>>> > R version 3.3.0 (2016-05-03)
>>> >
>>> > Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>> >
>>> > Running under: OS X 10.11.5 (El Capitan)
>>> >
>>> >
>>> > locale:
>>> >
>>> > [1] C/UTF-8/C/C/C/C
>>> >
>>> >
>>> > attached base packages:
>>> >
>>> > [1] stats graphics grDevices utils datasets methods base
>>> >
>>> >
>>> > other attached packages:
>>> >
>>> > [1] DNAcopy_1.46.0 aroma.light_3.2.0
>>> > aroma.affymetrix_3.0.0
>>> >
>>> > [4] aroma.core_3.0.0 R.devices_2.14.0 R.filesets_2.10.0
>>> >
>>> > [7] R.utils_2.3.0 R.oo_1.20.0affxparser_1.44.0
>>> >
>>> > [10] R.methodsS3_1.7.1 sfit_0.3.0
>>> >
>>> >
>>> > loaded via a namespace (and not attached):
>>> >
>>> > [1] matrixStats_0.50.2 codetools_0.2-14 listenv_0.6.0
>>> > future_1.0.0
>>> >
>>> > [5] digest_0.6.9 R.huge_0.9.0 PSCBS_0.61.0
>>>
Re: [aroma.affymetrix] CytoScanHD_Array: problems with CbsModel(), 'Failed to locate Class object for class 'FutureError'
Also, install the following version of the future package:
source("http://callr.org/install#HenrikBengtsson/future@FutureErrorFix";)
This should reveal the true underlying error message.
/Henrik
On Friday, July 1, 2016 at 11:09:36 AM UTC-7, Henrik Bengtsson wrote:
>
> Unfortunately, there's a "bug" in future 1.0.0 causing the actual
> error to be disguised as "Cannot get static instance. ..."; there
> should really be an informative error message, cf.
> https://github.com/HenrikBengtsson/future/issues/83.
>
> But your traceback gives some more information and I see you're using
> parallel processing, i.e. you're using:
>
> plan(multiprocess)
>
> somewhere at the beginning of your script, correct? As a starter,
> could you retry with:
>
> plan(eager)
>
> If that works / doesn't work, at least it'll give some more clues
> what's going on.
>
> In the meanwhile, I'll try to fix that future bug causing us not to
> see the actual error message. When I've got a working fix, I'll share
> a early-access version with you.
>
> /Henrik
>
>
>
> On Fri, Jul 1, 2016 at 8:02 AM, roman.hillje via aroma.affymetrix
> wrote:
> > Thanks for the comment. Unfortunately, the error persists even after the
> > updates. Here is the sessionInfo() output:
> >
> > R version 3.3.0 (2016-05-03)
> >
> > Platform: x86_64-apple-darwin13.4.0 (64-bit)
> >
> > Running under: OS X 10.11.5 (El Capitan)
> >
> >
> > locale:
> >
> > [1] C/UTF-8/C/C/C/C
> >
> >
> > attached base packages:
> >
> > [1] stats graphics grDevices utils datasets methods base
> >
> >
> > other attached packages:
> >
> > [1] DNAcopy_1.46.0 aroma.light_3.2.0
> aroma.affymetrix_3.0.0
> >
> > [4] aroma.core_3.0.0 R.devices_2.14.0 R.filesets_2.10.0
> >
> > [7] R.utils_2.3.0 R.oo_1.20.0affxparser_1.44.0
> >
> > [10] R.methodsS3_1.7.1 sfit_0.3.0
> >
> >
> > loaded via a namespace (and not attached):
> >
> > [1] matrixStats_0.50.2 codetools_0.2-14 listenv_0.6.0
> future_1.0.0
> >
> > [5] digest_0.6.9 R.huge_0.9.0 PSCBS_0.61.0
> tools_3.3.0
> >
> > [9] R.cache_0.12.0 parallel_3.3.0 base64enc_0.1-3
> > aroma.apd_0.6.0
> >
> > [13] R.rsp_0.30.0 globals_0.6.1
> >
> >
> > I tried running fit(cbs) - which I'm sure is the same getRegions() would
> do
> > ultimately. Here are the error messages and the traceback:
> >
> > fit(cbs)
> >
> >
> > Attaching package: ‘future’
> >
> >
> > The following object is masked from ‘package:R.utils’:
> >
> >
> > %<-%
> >
> >
> >
> > Attaching package: ‘future’
> >
> >
> > The following object is masked from ‘package:R.utils’:
> >
> >
> > %<-%
> >
> >
> >
> > Attaching package: ‘future’
> >
> >
> > The following object is masked from ‘package:R.utils’:
> >
> >
> > %<-%
> >
> >
> >
> > Attaching package: ‘future’
> >
> >
> > The following object is masked from ‘package:R.utils’:
> >
> >
> > %<-%
> >
> >
> >
> > Attaching package: ‘future’
> >
> >
> > The following object is masked from ‘package:R.utils’:
> >
> >
> > %<-%
> >
> >
> > Error in getStaticInstance.Object(this) :
> >
> > Cannot get static instance. Failed to locate Class object for class
> > 'FutureError'.
> >
> >
> > traceback:
> >
> >
> > 24: stop("Cannot get static instance. Failed to locate Class object for
> > class '",
> >
> > className, "'.")
> >
> > 23: getStaticInstance.Object(this)
> >
> > 22: getStaticInstance(this)
> >
> > 21: .getStaticInstance(this, static = static)
> >
> > 20: `$.Object`(c, "message")
> >
> > 19: c$message
> >
> > 18: conditionMessage.condition(cond)
> >
> > 17: conditionMessage(cond)
> >
> > 16: stop(FutureError(value, future = future))
> >
> > 15: value.Future(future)
> >
> > 14: NextMethod("value")
> >
> > 13: value.MulticoreFut
Re: [aroma.affymetrix] CytoScanHD_Array: problems with CbsModel(), 'Failed to locate Class object for class 'FutureError'
Unfortunately, there's a "bug" in future 1.0.0 causing the actual
error to be disguised as "Cannot get static instance. ..."; there
should really be an informative error message, cf.
https://github.com/HenrikBengtsson/future/issues/83.
But your traceback gives some more information and I see you're using
parallel processing, i.e. you're using:
plan(multiprocess)
somewhere at the beginning of your script, correct? As a starter,
could you retry with:
plan(eager)
If that works / doesn't work, at least it'll give some more clues
what's going on.
In the meanwhile, I'll try to fix that future bug causing us not to
see the actual error message. When I've got a working fix, I'll share
a early-access version with you.
/Henrik
On Fri, Jul 1, 2016 at 8:02 AM, roman.hillje via aroma.affymetrix
wrote:
> Thanks for the comment. Unfortunately, the error persists even after the
> updates. Here is the sessionInfo() output:
>
> R version 3.3.0 (2016-05-03)
>
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>
> Running under: OS X 10.11.5 (El Capitan)
>
>
> locale:
>
> [1] C/UTF-8/C/C/C/C
>
>
> attached base packages:
>
> [1] stats graphics grDevices utils datasets methods base
>
>
> other attached packages:
>
> [1] DNAcopy_1.46.0 aroma.light_3.2.0 aroma.affymetrix_3.0.0
>
> [4] aroma.core_3.0.0 R.devices_2.14.0 R.filesets_2.10.0
>
> [7] R.utils_2.3.0 R.oo_1.20.0affxparser_1.44.0
>
> [10] R.methodsS3_1.7.1 sfit_0.3.0
>
>
> loaded via a namespace (and not attached):
>
> [1] matrixStats_0.50.2 codetools_0.2-14 listenv_0.6.0 future_1.0.0
>
> [5] digest_0.6.9 R.huge_0.9.0 PSCBS_0.61.0 tools_3.3.0
>
> [9] R.cache_0.12.0 parallel_3.3.0 base64enc_0.1-3
> aroma.apd_0.6.0
>
> [13] R.rsp_0.30.0 globals_0.6.1
>
>
> I tried running fit(cbs) - which I'm sure is the same getRegions() would do
> ultimately. Here are the error messages and the traceback:
>
> fit(cbs)
>
>
> Attaching package: ‘future’
>
>
> The following object is masked from ‘package:R.utils’:
>
>
> %<-%
>
>
>
> Attaching package: ‘future’
>
>
> The following object is masked from ‘package:R.utils’:
>
>
> %<-%
>
>
>
> Attaching package: ‘future’
>
>
> The following object is masked from ‘package:R.utils’:
>
>
> %<-%
>
>
>
> Attaching package: ‘future’
>
>
> The following object is masked from ‘package:R.utils’:
>
>
> %<-%
>
>
>
> Attaching package: ‘future’
>
>
> The following object is masked from ‘package:R.utils’:
>
>
> %<-%
>
>
> Error in getStaticInstance.Object(this) :
>
> Cannot get static instance. Failed to locate Class object for class
> 'FutureError'.
>
>
> traceback:
>
>
> 24: stop("Cannot get static instance. Failed to locate Class object for
> class '",
>
> className, "'.")
>
> 23: getStaticInstance.Object(this)
>
> 22: getStaticInstance(this)
>
> 21: .getStaticInstance(this, static = static)
>
> 20: `$.Object`(c, "message")
>
> 19: c$message
>
> 18: conditionMessage.condition(cond)
>
> 17: conditionMessage(cond)
>
> 16: stop(FutureError(value, future = future))
>
> 15: value.Future(future)
>
> 14: NextMethod("value")
>
> 13: value.MulticoreFuture(future)
>
> 12: value(future)
>
> 11: eval(expr, envir, enclos)
>
> 10: eval(quote({
>
> value <- value(future)
>
> rm(list = future_name, envir = assign.env)
>
> value
>
> }), new.env())
>
> 9: eval(expr, envir, enclos)
>
> 8: eval(expr, p)
>
> 7: eval.parent(substitute(eval(quote(expr), envir)))
>
> 6: local({
>
>value <- value(future)
>
>rm(list = future_name, envir = assign.env)
>
>value
>
>})
>
> 5: mget(vars[ok], envir = x, inherits = FALSE)
>
> 4: as.list.listenv(res)
>
> 3: as.list(res)
>
> 2: fit.CopyNumberSegmentationModel(cbs)
>
> 1: fit(cbs)
>
>
> I think it's pretty obvious that simply the xdr-files are missing, I just
> don't know why.
>
> On Friday, July 1, 2016 at 4:34:22 PM UTC+2, Henrik Bengtsson wrote:
>>
>> Quick comment: Make sure all your packages are up-to-date and retry.
>> If that doesn't work, please post your sessionInfo() after you get the
>> error.
>>
>> /Henrik
>>
>> On Wed, Jun 29, 2016 at 1:32 AM, roman.hillje via aroma.affymetrix
>> wro
Re: [aroma.affymetrix] CytoScanHD_Array: problems with CbsModel(), 'Failed to locate Class object for class 'FutureError'
Quick comment: Make sure all your packages are up-to-date and retry.
If that doesn't work, please post your sessionInfo() after you get the
error.
/Henrik
On Wed, Jun 29, 2016 at 1:32 AM, roman.hillje via aroma.affymetrix
wrote:
> Hi,
>
> I'm currently trying to set up the analysis of CytoScanHD arrays through the
> aroma pipeline but ran into an issue with the CbsModel function. I prepared
> my sample and reference set so that I end up with this:
>
> sample set:
>
> CnChipEffectSet:
>
> Name: GSE69632
>
> Tags: ACC,ra,-XY,BPN,-XY,RMA,A+B
>
> Path: plmData/GSE69632,ACC,ra,-XY,BPN,-XY,RMA,A+B/CytoScanHD_Array
>
> Platform: Affymetrix
>
> Chip type: CytoScanHD_Array,monocell
>
> Number of arrays: 5
>
> Names: GSM1704973, GSM1704988, GSM1704989, GSM1704990, GSM1704991 [5]
>
> Time period: 2016-06-27 14:51:08 -- 2016-06-27 14:51:11
>
> Total file size: 173.14MB
>
> RAM: 0.01MB
>
> Parameters: {}
>
>
> reference set:
>
>
> CnChipEffectSet:
>
> Name: referenceSet
>
> Tags: ACC,ra,-XY,BPN,-XY,RMA,A+B
>
> Path: plmData/referenceSet,ACC,ra,-XY,BPN,-XY,RMA,A+B/CytoScanHD_Array
>
> Platform: Affymetrix
>
> Chip type: CytoScanHD_Array,monocell
>
> Number of arrays: 5
>
> Names: .baseline, .baseline, .baseline, .baseline, .baseline [5]
>
> Time period: 2016-06-28 12:05:09 -- 2016-06-28 12:05:09
>
> Total file size: 173.14MB
>
> RAM: 0.01MB
>
> Parameters: {}
>
>
> Then I do 'cbs <- CbsModel(sampleSet, referenceSet)' and get the following
> output:
>
>
> CbsModel:
>
> Name: GSE69632
>
> Tags: ACC,ra,-XY,BPN,-XY,RMA,A+B,paired
>
> Chip type (virtual): CytoScanHD_Array
>
> Path: cbsData/GSE69632,ACC,ra,-XY,BPN,-XY,RMA,A+B,paired/CytoScanHD_Array
>
> Number of chip types: 1
>
> Sample & reference file pairs:
>
> Chip type #1 ('CytoScanHD_Array') of 1:
>
> Sample data set:
>
> CnChipEffectSet:
>
> Name: GSE69632
>
> Tags: ACC,ra,-XY,BPN,-XY,RMA,A+B
>
> Path: plmData/GSE69632,ACC,ra,-XY,BPN,-XY,RMA,A+B/CytoScanHD_Array
>
> Platform: Affymetrix
>
> Chip type: CytoScanHD_Array,monocell
>
> Number of arrays: 5
>
> Names: GSM1704973, GSM1704988, GSM1704989, GSM1704990, GSM1704991 [5]
>
> Time period: 2016-06-27 14:51:08 -- 2016-06-27 14:51:11
>
> Total file size: 173.14MB
>
> RAM: 0.01MB
>
> Parameters: {}
>
> Reference data set/file:
>
> CnChipEffectSet:
>
> Name: referenceSet
>
> Tags: ACC,ra,-XY,BPN,-XY,RMA,A+B
>
> Path: plmData/referenceSet,ACC,ra,-XY,BPN,-XY,RMA,A+B/CytoScanHD_Array
>
> Platform: Affymetrix
>
> Chip type: CytoScanHD_Array,monocell
>
> Number of arrays: 5
>
> Names: .baseline, .baseline, .baseline, .baseline, .baseline [5]
>
> Time period: 2016-06-28 12:05:09 -- 2016-06-28 12:05:09
>
> Total file size: 173.14MB
>
> RAM: 0.01MB
>
> Parameters: {}
>
> RAM: 0.00MB
>
>
> Until here everything is fine, but when trying to run getRegions() on the
> CbsModel I receive an error:
>
>
> reg <- getRegions(cbs, arrays=1, chromosomes=1:22,
> verbose=Arguments$getVerbose(-1))
>
> Extracting regions from all fits...
>
> Obtaining CN model fits (or fit if missing)...
>
> Error in getStaticInstance.Object(this) :
>
> Cannot get static instance. Failed to locate Class object for class
> 'FutureError'.
>
> Obtaining CN model fits (or fit if missing)...done
>
> Extracting regions from all fits...done
>
>
> Does anybody know what the issue could be? I suspect it has to do with the
> CbsModel because the respective folder
> (cbsData/GSE69632,ACC,ra,-XY,BPN,-XY,RMA,A+B,paired/CytoScanHD_Array) stays
> empty even though attempted to be modified at the time of running the
> getRegions command.
>
>
> I would really appreciate input/feedback/ideas since I'm relatively new to
> the topic :)
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> ---
> You received this message because you are subscribed to the Google Groups
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> To unsubscribe from this group and stop receiving emails from it, send an
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> For more options, visit https://groups.google.com/d/optout.
--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
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---
You received this message becau
Re: [aroma.affymetrix] "Error: Failed to retrieve genome information" + paired samples
Hi,
comments below.
On Fri, May 13, 2016 at 10:24 AM, Gaius Augustus
wrote:
> Hello,
> I'm working on the Paired PSCBS protocol, and am running across an error.
>
> Here is my file structure
>
> -annotationData
> ---chipTypes
> -GenomeWideSNP_6
> ---GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118.ufl
> ---GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118.ugp
> ---GenomeWideSNP_6,Full.cdf
> ---GenomeWideSNP_6,HB20080710.acs
> ---GenomeWideSNP_6.cdf
> -rawData
> ---Samples
> -GenomeWideSNP_6
> ---LIST OF CEL FILES
This is all correct, except that "Samples" is not very descriptive
name for a data set - try to pick a better name (although it won't
affect your analysis).
So, the GenomeWideSNP_6 chip type is special in the sense that
Affymetrix provide two different CDF for it: the default one and the
"full" one. You have both in
annotationData/chipTypes/GenomeWideSNP_6/, which is nothing strange
and that is the correct (and only) place to put them.
The problem you're having is that you didn't tell Aroma to use the
"full" CDF, so it's going with the "default" one. This is why you're
seeing "Chip type: GenomeWideSNP_6" in:
> AffymetrixCelSet:
> Name: Samples
> Tags:
> Path: rawData/Samples/GenomeWideSNP_6
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6
> Number of arrays: 116
> [...]
(and not "Chip type: GenomeWideSNP_6,full"). So, later Aroma wants to
access the other type of annotation data, it cannot find anything,
because the ones you have are only the ones for the "full" CDF.
That's why get the error.
You don't show how you set up your AffymetrixCelSet `csR` object, but
you there are basically two ways to do it. You can either set up the
AffymetrixCdfSet `cdf` explicitly and pass that when you set up the
`csR` object, or you can do both in one step. I typically do:
cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
csR <- AffymetrixCelSet$byName("Samples", cdf=cdf)
because that is very explicit about which CDF is being used. You can
also do these two in one step as:
csR <- AffymetrixCelSet$byName("Samples", chipType="GenomeWideSNP_6,full")
But again, I think the first approach is much clearer. This is also
what http://www.aroma-project.org/vignettes/CRMAv2/ uses. If you look
at that vignette, it also calls getGenomeInformation(cdf) etc at the
very beginning. A user don't really need to call those, because
they'll be call internally as needed. Instead they are there just to
assert that you have all needed annotation data up front and that
Aroma can find them. So, if you call those on the "full" CDF, you
shouldn't get any errors. If so, then you know you're ready to go.
Hope this helps to get you started
Henrik
>
>
>
> Everything seems to work fine in the Paired PSCBS protocol (except for one
> thing, which I'll ask at the end), until I run:
>
> res <- doASCRMAv2(csR, verbose=verbose)
>
> 20160512 16:56:04|CRMAv2...
> 20160512 16:56:04| Arguments:
> 20160512 16:56:04| combineAlleles: FALSE
> 20160512 16:56:04| arrays:
> chr ""
> 20160512 16:56:04| Data set
> AffymetrixCelSet:
> Name: Samples
> Tags:
> Path: rawData/Samples/GenomeWideSNP_6
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6
> Number of arrays: 116
> Names: TCGA-3L-AA1B_Normal_Black, TCGA-3L-AA1B_Tumor_Black,
> TCGA-4N-A93T_Normal_Black, ..., TCGA-WS-AB45_Tumor_Black [116]
> Time period: 2011-03-08 10:19:00 -- 2014-08-21 11:25:30
> Total file size: 7645.59MB
> RAM: 0.14MB
> 20160512 16:56:10| Checking whether final results are available or not...
> 20160512 16:56:10| Checking whether final results are available or
> not...done
> 20160512 16:56:10| CRMAv2/Allelic crosstalk calibration...
> [2016-05-12 16:56:11] Exception: Failed to retrieve genome information for
> this chip type: GenomeWideSNP_6
>
>
> at #28. getGenomeInformation.AffymetrixCdfFile(cdf)
> - getGenomeInformation.AffymetrixCdfFile() is in environment
> 'aroma.affymetrix'
>
>
> at #27. getGenomeInformation(cdf)
> - getGenomeInformation() is in environment 'aroma.affymetrix'
>
>
> at #26. getSubsetToAvg.AllelicCrosstalkCalibration(this)
> - getSubsetToAvg.AllelicCrosstalkCalibration() is in environment
> 'aroma.affymetrix'
>
>
> at #25. getSubsetToAvg(this)
> - getSubsetToAvg() is in environment 'aroma.affymetrix'
>
>
> at #24. getParameters.AllelicCrosstalkCalibration(this, ...)
> - getParameters.AllelicCrosstalkCalibration() is in environment
> 'aroma.affymetrix'
>
>
> at #23. getParameters(this, ...)
> - getParameters() is in environment 'aroma.core'
>
>
> at #22. getParameterSets.ParametersInterface(this, ..., drop = FALSE)
> - getParameterSets.ParametersInterface() is in environment
> 'aroma.core'
>
>
> at #21. getParameterSets(this, ..., drop = FALSE)
> - getParameterSets() is in environment 'aroma.core'
>
>
> at #20. getParametersAsString.ParametersInterface(this)
> -
Re: [aroma.affymetrix] Incorporating Tumor Purity for ASCRMA / PSCBS
In the PSCBS package, we provide the `estimateKappa()` function for estimating kappa, which we refer to as "background signal", cf. https://cran.r-project.org/web/packages/PSCBS/vignettes/PairedPSCBS.pdf. The kappa parameter is strongly correlated with the amount of normal contamination. We're very conservative in claiming it equals the normal contamination, because in order for that to be an accurate estimator we need to assume strong linearity in signals, which we don't want to claim. This is also why we keep 'kappa' somewhat under the radar. However, if you ignore this, you can treat kappa as an estimator for amount of normal contamination (others do that in other methods). In addition, it's pretty safe to say that kappa preserves the rank of the true normal contamination, that is, you can fairly safely compare kappa between samples and conclude that one sample has more normal contamination that another. What you cannot say for sure is the exact amount, which might be important when your trying to use it to control mutation rates etc. Hope this helps Henrik On Fri, Apr 22, 2016 at 11:47 AM, Kevin McCormick wrote: > Is there a way to incorporate tumor purity estimates (e.g. from ASCAT) into > the Aroma pipeline for segmenting copy number changes between parent and > tumor? We are looking at cell lines derived from tumors to compare > consistency between copy number variations. The tumor purity in the > parental cells has moderate variation, and the lines with lower purity in > the parental are getting called to have more copy number changes than those > with higher purity, even though a manual inspection suggests the differences > are merely due to change in purity. > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median
Good to hear. /Henrik
On Fri, Mar 25, 2016 at 10:11 AM, C.C. wrote:
> I installed R 3.2.3 (don't know why unable to install R 3.2.4) and then
> reinstalled aroma.affymetrix 3.0. It worked!
> Thanks Henrik!
>
> On Thursday, March 24, 2016 at 2:16:57 PM UTC-7, Henrik Bengtsson wrote:
>>
>> You most likely got an error during installation, because
>> aroma.affymetrix now requires R (≥ 3.1.2) -
>> https://cran.r-project.org/web/packages/aroma.affymetrix/ - and you're
>> on R 3.1.0, which is nearly two years old.
>>
>> The solution is to update to a recent version of R, i.e. R 3.2.4.
>> FYI, R 3.3.0 is coming in a few weeks.
>>
>> /Henrik
>>
>> On Thu, Mar 24, 2016 at 2:12 PM, Henrik Bengtsson
>> wrote:
>> > On Thu, Mar 24, 2016 at 1:54 PM, C.C. wrote:
>> >> Hi Henrik,
>> >>
>> >> Thanks for you email. Here is the problem I encountered.
>> >>
>> >>
>> >>
>> >> I installed the package using, it is the latest version 3.0.0
>> >>
>> >>
>> >> source('http://callr.org/install#aroma.affymetrix')
>> >
>> > Did you get errors and did you make sure you restarted R, because your
>> > session information below says you're still running lots of outdated
>> > versions, e.g. aroma.affymetrix_2.13.1.
>> >
>> > /Henrik
>> >
>> >>
>> >>
>> >>
>> >> and I was trying to run doCRMAv2
>> >>
>> >> dsList <- doCRMAv2(cel.subset, cdf=cdf,
>> >> verbose=Arguments$getVerbose(-10, timestamp=TRUE))
>> >>
>> >>
>> >>
>> >> and then got error information
>> >>
>> >>> > >>> renamed
>> >>> to 'center'. Please update code accordingly.>
>> >>>
>> >>> [2016-03-24 13:12:44] Exception: The fit function for requested AvgPlm
>> >>> flavor failed: median
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> at #08. getFitUnitGroupFunction.AvgPlm(this, ...)
>> >>>
>> >>> - getFitUnitGroupFunction.AvgPlm() is in environment
>> >>> 'aroma.affymetrix'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> at #07. getFitUnitGroupFunction(this, ...)
>> >>>
>> >>> - getFitUnitGroupFunction() is in environment
>> >>> 'aroma.affymetrix'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> at #06. getFitUnitFunction.CnPlm(this)
>> >>>
>> >>> - getFitUnitFunction.CnPlm() is in environment
>> >>> 'aroma.affymetrix'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> at #05. getFitUnitFunction(this)
>> >>>
>> >>> - getFitUnitFunction() is in environment 'aroma.affymetrix'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> at #04. fit.ProbeLevelModel(plm, verbose = verbose)
>> >>>
>> >>> - fit.ProbeLevelModel() is in environment 'aroma.affymetrix'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> at #03. fit(plm, verbose = verbose)
>> >>>
>> >>> - fit() is in environment 'aroma.core'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> at #02. doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose =
>> >>> Arguments$getVerbose(-10,
>> >>>
>> >>> timestamp = TRUE))
>> >>>
>> >>> - doCRMAv2.AffymetrixCelSet() is in environment
>> >>> 'aroma.affymetrix'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> at #01. doCRMAv2(cel.subset, cdf = cdf, verbose =
>> >>> Arguments$getVerbose(-10,
>> >>>
>> >>> timestamp = TRUE))
>> >>>
>> >>> - doCRMAv2() is in environment 'aroma.affymetrix'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> Error: The fit function for requested AvgPlm flavor failed: median
>> >>
Re: [aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median
You most likely got an error during installation, because
aroma.affymetrix now requires R (≥ 3.1.2) -
https://cran.r-project.org/web/packages/aroma.affymetrix/ - and you're
on R 3.1.0, which is nearly two years old.
The solution is to update to a recent version of R, i.e. R 3.2.4.
FYI, R 3.3.0 is coming in a few weeks.
/Henrik
On Thu, Mar 24, 2016 at 2:12 PM, Henrik Bengtsson
wrote:
> On Thu, Mar 24, 2016 at 1:54 PM, C.C. wrote:
>> Hi Henrik,
>>
>> Thanks for you email. Here is the problem I encountered.
>>
>>
>>
>> I installed the package using, it is the latest version 3.0.0
>>
>>
>> source('http://callr.org/install#aroma.affymetrix')
>
> Did you get errors and did you make sure you restarted R, because your
> session information below says you're still running lots of outdated
> versions, e.g. aroma.affymetrix_2.13.1.
>
> /Henrik
>
>>
>>
>>
>> and I was trying to run doCRMAv2
>>
>> dsList <- doCRMAv2(cel.subset, cdf=cdf,
>> verbose=Arguments$getVerbose(-10, timestamp=TRUE))
>>
>>
>>
>> and then got error information
>>
>>> >> renamed
>>> to 'center'. Please update code accordingly.>
>>>
>>> [2016-03-24 13:12:44] Exception: The fit function for requested AvgPlm
>>> flavor failed: median
>>>
>>>
>>>
>>>
>>> at #08. getFitUnitGroupFunction.AvgPlm(this, ...)
>>>
>>> - getFitUnitGroupFunction.AvgPlm() is in environment
>>> 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>> at #07. getFitUnitGroupFunction(this, ...)
>>>
>>> - getFitUnitGroupFunction() is in environment 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>> at #06. getFitUnitFunction.CnPlm(this)
>>>
>>> - getFitUnitFunction.CnPlm() is in environment
>>> 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>> at #05. getFitUnitFunction(this)
>>>
>>> - getFitUnitFunction() is in environment 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>> at #04. fit.ProbeLevelModel(plm, verbose = verbose)
>>>
>>> - fit.ProbeLevelModel() is in environment 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>> at #03. fit(plm, verbose = verbose)
>>>
>>> - fit() is in environment 'aroma.core'
>>>
>>>
>>>
>>>
>>> at #02. doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose =
>>> Arguments$getVerbose(-10,
>>>
>>> timestamp = TRUE))
>>>
>>> - doCRMAv2.AffymetrixCelSet() is in environment
>>> 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>> at #01. doCRMAv2(cel.subset, cdf = cdf, verbose =
>>> Arguments$getVerbose(-10,
>>>
>>> timestamp = TRUE))
>>>
>>> - doCRMAv2() is in environment 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>> Error: The fit function for requested AvgPlm flavor failed: median
>>>
>>> 20160324 13:12:44| Setting up parameter sets...done
>>>
>>> 20160324 13:12:44| Fitting model of class AvgCnPlm...done
>>>
>>>>
>>>
>> traceback()
>>
>>
>>>
>>> 13: stop(cond)
>>>
>>> 12: throw.Exception(Exception(...))
>>>
>>> 11: throw(Exception(...))
>>>
>>> 10: throw.default("The fit function for requested AvgPlm flavor failed: ",
>>>
>>> flavor)
>>>
>>> 9: throw("The fit function for requested AvgPlm flavor failed: ",
>>>
>>>flavor)
>>>
>>> 8: getFitUnitGroupFunction.AvgPlm(this, ...)
>>>
>>> 7: getFitUnitGroupFunction(this, ...)
>>>
>>> 6: getFitUnitFunction.CnPlm(this)
>>>
>>> 5: getFitUnitFunction(this)
>>>
>>> 4: fit.ProbeLevelModel(plm, verbose = verbose)
>>>
>>> 3: fit(plm, verbose = verbose)
>>>
>>> 2: doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose = v)
>>>
>>> 1: doCRMAv2(cel.subset, cdf = cdf, verbose = v)
>>>
>>>
>> sessionInfo()
>>
>>
>>>
>>> R version 3.1.0 (2014-04-10)
>>>
>>> Platform: x86_64-r
Re: [aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median
On Thu, Mar 24, 2016 at 1:54 PM, C.C. wrote:
> Hi Henrik,
>
> Thanks for you email. Here is the problem I encountered.
>
>
>
> I installed the package using, it is the latest version 3.0.0
>
>
> source('http://callr.org/install#aroma.affymetrix')
Did you get errors and did you make sure you restarted R, because your
session information below says you're still running lots of outdated
versions, e.g. aroma.affymetrix_2.13.1.
/Henrik
>
>
>
> and I was trying to run doCRMAv2
>
> dsList <- doCRMAv2(cel.subset, cdf=cdf,
> verbose=Arguments$getVerbose(-10, timestamp=TRUE))
>
>
>
> and then got error information
>
>> > renamed
>> to 'center'. Please update code accordingly.>
>>
>> [2016-03-24 13:12:44] Exception: The fit function for requested AvgPlm
>> flavor failed: median
>>
>>
>>
>>
>> at #08. getFitUnitGroupFunction.AvgPlm(this, ...)
>>
>> - getFitUnitGroupFunction.AvgPlm() is in environment
>> 'aroma.affymetrix'
>>
>>
>>
>>
>> at #07. getFitUnitGroupFunction(this, ...)
>>
>> - getFitUnitGroupFunction() is in environment 'aroma.affymetrix'
>>
>>
>>
>>
>> at #06. getFitUnitFunction.CnPlm(this)
>>
>> - getFitUnitFunction.CnPlm() is in environment
>> 'aroma.affymetrix'
>>
>>
>>
>>
>> at #05. getFitUnitFunction(this)
>>
>> - getFitUnitFunction() is in environment 'aroma.affymetrix'
>>
>>
>>
>>
>> at #04. fit.ProbeLevelModel(plm, verbose = verbose)
>>
>> - fit.ProbeLevelModel() is in environment 'aroma.affymetrix'
>>
>>
>>
>>
>> at #03. fit(plm, verbose = verbose)
>>
>> - fit() is in environment 'aroma.core'
>>
>>
>>
>>
>> at #02. doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose =
>> Arguments$getVerbose(-10,
>>
>> timestamp = TRUE))
>>
>> - doCRMAv2.AffymetrixCelSet() is in environment
>> 'aroma.affymetrix'
>>
>>
>>
>>
>> at #01. doCRMAv2(cel.subset, cdf = cdf, verbose =
>> Arguments$getVerbose(-10,
>>
>> timestamp = TRUE))
>>
>> - doCRMAv2() is in environment 'aroma.affymetrix'
>>
>>
>>
>>
>> Error: The fit function for requested AvgPlm flavor failed: median
>>
>> 20160324 13:12:44| Setting up parameter sets...done
>>
>> 20160324 13:12:44| Fitting model of class AvgCnPlm...done
>>
>>>
>>
> traceback()
>
>
>>
>> 13: stop(cond)
>>
>> 12: throw.Exception(Exception(...))
>>
>> 11: throw(Exception(...))
>>
>> 10: throw.default("The fit function for requested AvgPlm flavor failed: ",
>>
>> flavor)
>>
>> 9: throw("The fit function for requested AvgPlm flavor failed: ",
>>
>>flavor)
>>
>> 8: getFitUnitGroupFunction.AvgPlm(this, ...)
>>
>> 7: getFitUnitGroupFunction(this, ...)
>>
>> 6: getFitUnitFunction.CnPlm(this)
>>
>> 5: getFitUnitFunction(this)
>>
>> 4: fit.ProbeLevelModel(plm, verbose = verbose)
>>
>> 3: fit(plm, verbose = verbose)
>>
>> 2: doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose = v)
>>
>> 1: doCRMAv2(cel.subset, cdf = cdf, verbose = v)
>>
>>
> sessionInfo()
>
>
>>
>> R version 3.1.0 (2014-04-10)
>>
>> Platform: x86_64-redhat-linux-gnu (64-bit)
>>
>>
>> locale:
>>
>> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
>> LC_TIME=en_US.iso885915LC_COLLATE=en_US.iso885915
>> LC_MONETARY=en_US.iso885915LC_MESSAGES=en_US.iso885915
>> LC_PAPER=en_US.iso885915
>>
>> [8] LC_NAME=C LC_ADDRESS=C
>> LC_TELEPHONE=C LC_MEASUREMENT=en_US.iso885915
>> LC_IDENTIFICATION=C
>>
>>
>> attached base packages:
>>
>> [1] stats graphics grDevices utils datasets methods base
>>
>>
>> other attached packages:
>>
>> [1] sfit_0.3.0 aroma.light_2.0.0 matrixStats_0.50.1
>> aroma.affymetrix_2.13.1 aroma.core_2.13.0 R.devices_2.14.0
>> R.filesets_2.6.0R.utils_2.2.0 R.oo_1.20.0
>> affxparser_1.36.0
>>
>> [11] R.methodsS3_1.7.1
>>
>>
>> loaded via a namespace (and not attach
Re: [aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median
Hi, in order for us to help you, could you please: "[...] make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example." Thanks, Henrik On Thu, Mar 24, 2016 at 9:59 AM, C.C. wrote: > Hello, > > I was trying to run doCRMAv2.R in aroma.affymetrix 3.0 and get the error. > Dose anyone know what is the problem? Thanks. > > > > Error: The fit function for requested AvgPlm flavor failed: median > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] Extracting probe level intensities
Hi, just exclude argument 'cells', i.e. data <- extractMatrix(cs) This will reads all cells/probes. Henrik On Mar 2, 2016 05:47, "sanj" wrote: > Hi, > > I was wondering if its possible to extract probe level intensities from > cel files without depending on a particular CDF file? > > At the moment I am using: > > df <- readDataFrame(getCdf(cs), verbose=-80) > raw<-extractMatrix(cs,cells=df$cell,verbose=verbose) > > But its dependent on the CDF file thus we will only have probes that are > included within the CDF. However we want the intensities for all > probes irrespective of the CDF used. > > Is this possible in aroma.affymetrix? > > Regards, > Sanj > > > > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the > latest version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to > http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] Re: CbsModel parameters
Hi, I've bbc:ed Venkat since I don't know if he's on this list or not. I don't have any particular suggestions for tweaking the default DNAcopy::segment() CBS parameters. If you missed it, both aroma.affymetrix and PSCBS now supports parallel process to some extent, cf. http://www.aroma-project.org/howtos/parallel_processing/ /Henrik On Tue, Feb 2, 2016 at 6:28 AM, mbaudis wrote: > Hi Hendrik, Venkat, > > we're about to start a large processing run (>20k Affy arrays from GEO, > various platforms). Good time to review/update our old pipeline ... > > What is the best way/recomm. parameters now for the min.width argument, and > has the cbs part been modified? Any recommendation to do platform specific > adjustements (majority are 250k & SNP6)? > > Pointers appreciated! > > Thanks & best, > > Michael. > > On Wednesday, October 27, 2010 at 9:19:24 PM UTC+2, Venkat wrote: >> >> This can happen occasionally. The min.width argument specifies the >> minimum number of probes in the minor arc of the circular (remember this is >> circular binary segmentation). So if you can get 2 probes from one end and >> 3 from the other to be significantly different the middle you will get a >> significant result and a segmentation. I need to change the code in order >> to eliminate this possibility. >> >> Venkat >> >> >> On Wed, Oct 27, 2010 at 2:32 PM, Henrik Bengtsson >> wrote: >>> >>> Are you sure you are not picking up old results, that is, did you use >>> fit(cbs, ..., force=TRUE) or simply did you remove the previous >>> segmentation results in cbsData/? >>> >>> You can troubleshoot with one array and one chromosome, e.g. >>> >>> fit(cbs, arrays=6, chromosomes=16, min.width=5, undo.splits="sdundo", >>> undo.SD=1, force=TRUE, verbose=-10); >>> >>> /Henrik >>> >>> On Wed, Oct 27, 2010 at 11:20 AM, Kai wrote: >>> > Hi Henrik, >>> > >>> > Thank you for your reply. However, I followed your instructions but >>> > still got segments with only 2 markers: >>> > >>> > These are the codes I ran: >>> > >>> > cbs = CbsModel(ds); >>> > cbs$.calculateRatios = FALSE; >>> > fit(cbs, chromosomes=c(1:23), min.width=5, undo.splits="sdundo", >>> > undo.SD=1, verbose=-10); >>> > ce = ChromosomeExplorer(cbs); >>> > process(ce,chromosomes=c(1:23)); >>> > >>> > These are what I found out in the results (there are a total of 4 >>> > samples): >>> > >>> >> min(getRegions(cbs)[[1]][,5]) >>> > [1] 5 >>> >> min(getRegions(cbs)[[2]][,5]) >>> > [1] 2 >>> >> min(getRegions(cbs)[[3]][,5]) >>> > [1] 2 >>> >> min(getRegions(cbs)[[4]][,5]) >>> > [1] 2 >>> >> which(getRegions(cbs)[[4]][,5]==2) >>> > [1] 52 139 >>> >> getRegions(cbs)[[4]][139,1:5] >>> >chromosomestart stop mean count >>> > 139 16 45057510 45057696 -1.427 2 >>> > >>> > It seems to me that min.width=5 worked only in the first sample. Do >>> > you have any idea on this? Thanks! >>> > >>> > Best, >>> > Kai >>> > >>> > >>> > On Oct 26, 9:09 pm, Henrik Bengtsson >> > project.org> wrote: >>> >> I forgot to say that in the next release of aroma.core package, you >>> >> will be able to specify additional arguments when you setup the CBS >>> >> model: >>> >> >>> >> cbs <- CbsModel(ds, min.width=5); >>> >> >>> >> ...but until then you have to stick with the below workaround. >>> >> >>> >> /Henrik >>> >> >>> >> On Tue, Oct 26, 2010 at 9:07 PM, hb wrote: >>> >> > Hi, >>> >> >>> >> > sorry my mistake. I meant to write that you should pass the >>> >> > additional arguments to fit() for the CbsModel (not process()), e.g. >>> >> >>> >> > cbs <- CbsModel(ds); >>> >> > cbs$.calculateRatios <- FALSE; >>> >> > fit(cbs, chromosomes=1:23, min.width=5, verbose=-10); >>> >> >>> >> > This will (explicitly) fit the segmentation model. Have a look at >>> >> > the verbose output; you'll see that "min.width" should show up
Re: [aroma.affymetrix] Error: object 'csC' not found.
On Sun, Jan 10, 2016 at 11:36 PM, wrote:
>
> Hi dear professor Henrik Bengtsson,
>
> When I was declaring the raw data set of CytoScan HD Array with
> aroma.affymetrix, I'm encountering the following errors:
>
> "Error: object 'csC' not found."
It seems like you didn't run the command before. Make sure each
object is actually created in every step by printing it, e.g.
print(cdf), etc. That should help you narrow down where your problem
is.
/Henrik
>
> I have searched the forum, unfortunately, I can't solve this problem.
>
> Could you give me some suggestions and help me solve it ?
>
> The following are the R code of mine:
>
> > setwd("G:/")
>
> >library("aroma.affymetrix")
>
> >log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>
> >options(digits=4)
>
> >cdf <- AffymetrixCdfFile$byChipType("CytoScanHD_Array")
>
> >gi <- getGenomeInformation(cdf)
>
> >si <- getSnpInformation(cdf)
>
> >acs <- AromaCellSequenceFile$byChipType(getChipType(cdf))
>
> >csR <- AffymetrixCelSet$byName("CytoScanHD_Array", cdf=cdf)
>
> >acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
>
> >csC <- process(acc, verbose=verbose)
>
> > print(csC)
>
> > sessionInfo()
> R version 3.2.2 (2015-08-14)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 7 x64 (build 7601) Service Pack 1
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] aroma.light_2.4.0 aroma.affymetrix_2.14.0 affxparser_1.42.0
> [4] aroma.core_3.0.0R.devices_2.13.2R.filesets_2.10.0
> [7] R.utils_2.2.0 R.oo_1.19.0 R.methodsS3_1.7.0
>
> loaded via a namespace (and not attached):
>
> [1] matrixStats_0.50.1 codetools_0.2-14 listenv_0.6.0 future_0.10.0
> [5] digest_0.6.8 R.huge_0.9.0 PSCBS_0.60.0 tools_3.2.2
> [9] R.cache_0.12.0 parallel_3.2.2 base64enc_0.1-3aroma.apd_0.6.0
> [13] R.rsp_0.21.0 globals_0.6.0 DNAcopy_1.42.0
>
> CEL format raw data are locate in
> "G:/rawData/CytoScanHD_Array/CytoScanHD_Array"
>
> Looking forward your replay. Thank you very much.
>
>
>
>
>
>
>
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> ---
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to aroma-affymetrix+unsubscr...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
---
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to aroma-affymetrix+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
[aroma.affymetrix] aroma.affymetrix 3.0.0 release (10 years today!) - now with parallel processing
The Aroma Project turns 10 years today. Technically it's probably a
few weeks older, but it was on Jan 11, 2006 that a few R scripts was
put together to create the aroma.affymetrix. To celebrate,
aroma.affymetrix 3.0.0 has been released and it brings some exiting
updates including parallel processing (finally!) and automatic
generation of checksum files. For full update details, see the end of
this message. To update, just do:
source("http://callr.org/install#aroma.affymetrix";)
Now to what everyone is wondering - how can we do parallel processing?
It is super easy because everything is taken care of internally, so
no need to change anything. All you have to do is specify what type
of processing you wish to use. To utilize multiple cores on the local
machine, just add (preferably to your ~/.Rprofile startup file):
future::plan("multicore")
That's all. Pretty neat, eh? For other types of parallel processing,
see http://aroma-project.org/howtos/parallel_processing/.
Enjoy,
Henrik
Details on updated since aroma.affymetrix 2.14.0 (2015-10-24).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Updates to aroma.affymetrix
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Version: 3.0.0 [2016-01-09]
o SPEED: Adding support for parallel/distributed processing via futures
to some of the methods for which it is possible to process each
sample independently, e.g. background and crosstalk correction methods.
o REPRODUCIBILITY: Several of the methods now generate *.md5 checksum
files for the data files they output.
o REPRODUCIBILITY: GcRmaBackgroundCorrection(), LimmaBackgroundCorrection(),
and RmaBackgroundCorrection() gained argument 'seed'.
o Package requires R (>= 3.1.2) and BioC (>= 3.0) both released
in October 2014.
o Now also convertToUnique() acknowledge asterisk tags.
o ROBUSTNESS: MatNormalization did not create CEL files atomically.
o ROBUSTNESS: Using do.call(fcn) internally instead of do.call("fcn").
o ROBUSTNESS: Using getPathname() instead of accessing private field.
o CLEANUP: Warnings on "is.na() applied to non-(list or vector) of
type 'NULL'" are no longer generated.
o CLEANUP: Formally defunct'ed bgAdjustRma(), bgAdjustGcrma(),
bgAdjustOptical() for AffymetrixCelFile/AffymetrixCelSet since they
have effectively been defunct'ed in the public API for years. These
are now all incorporated in corresponding BackgroundCorrection classes.
o BUG FIX: LimmaBackgroundCorrection(..., addJitter=TRUE) gave an error.
o BUG FIX: convertToUnique() for AffymetrixCelSet would give an error
if there was an error while checking if results already exist.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Updates to aroma.core
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Version: 3.0.0 [2016-01-05]
o SPEED: Segmentation methods (e.g. CbsModel) now uses futures, which
means that samples can now be segmented in parallel/distributed.
o Package requires R (>= 3.1.2) and BioC (>= 3.0) both released in
October 2014.
o ROBUSTNESS: Using do.call(fcn) internally instead of do.call("fcn").
o ROBUSTNESS: Using getPathname() instead of accessing private field.
o CLEANUP: Defunct apply() for SampleAnnotationFile; use applyTo().
o CLEANUP: Drop defunct methods.
o BUG FIX: getOutputDataSet(..., onMissing="dropall") for AromaTransform
would throw error on no applicable method getFullNames() for NULL.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Updates to R.filesets
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Version: 2.10.0 [2016-01-04]
o Now file sizes are reported using IEC binary prefixes, i.e.
bytes, KiB, MiB, GiB, TiB, ..., YiB.
o Preparing to make the default pathname for GenericDataFile() to
become NA_character_. It is currently NULL, but the goal is to
enforce length(pathname) to be one.
o Added hasChecksumFile() for GenericDataFile.
o hasBeenModified() for GenericDataFile gained argument 'update'.
o Package requires R (>= 3.1.2) released October 2014, because
of its dependency on the listenv package.
o CLEANUP: extractMatrix(ds, files, ...) for GenericTabularFileSet
is deprecated. Use extractMatrix(ds[files], ...) instead.
o CLEANUP: Removed na.omit() for GenericDataFileSet; the default
one in the stats package works equally well.
o ROBUSTNESS: Increased test coverage from 51% to 62%.
o BUG FIX: Arguments$getTags() failed to drop missing values.
o BUG FIX: equals(df, other) for GenericDataFile would give an error
if 'other' was not a GenericDataFile.
o BUG FIX: dropTags() would drop name if a tag had the same name.
o BUG FIX: getOneFile() on a GenericDataFileSet with a single
missing file would give an error, now it gives a file with
an NA pathname.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
PSCBS
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Version: 0.60.0 [2015-11-17]
o PARALLEL
Re: [aroma.affymetrix] Re: Affymetrix Oncoscan library files
Ok, so that complicates how one would look at the pre-processing and
how to normalize the signals, e.g. one should probably normalize probe
signals of the two CEL files separately and only merge them after this
step.
A small first step would be to see if you can create a spatial image
of the CEL files, e.g.
library("aroma.affymetrix")
df <- AffymetrixCelFile("rawData/FusionSDK_Test3/Test3/Test3-1-121502.CEL")
print(df)
## Display in R
img <- getImage(df)
display(img)
## Generate a PNG and view it
png <- writeImage(df)
browseURL(png)
/Henrik
On Thu, Nov 12, 2015 at 5:05 PM, Keith C wrote:
> the CEL files are generated from two separate chips and hybs.
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> ---
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to aroma-affymetrix+unsubscr...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
---
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"aroma.affymetrix" group.
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Re: [aroma.affymetrix] Re: Affymetrix Oncoscan library files
Actually, if there are regular CEL files outputted, and assuming they're not non-supported multi-channel CEL files, then it might not be an impossible task. There is still a need for a CDF though, but people have built CDF for Affymetrix chiptypes that don't official have CDFs. First question that comes to mind is whether the two CEL files are coming from a single hybridization/chip, or two separate hybridizations/chips. If from a single one, then one could imagine creating a virtual chip where one start by merging the data from the two CEL files into one bigger CEL file. Likewise, one can then create one CDF file for this virtual file. From there, low-level affxparser should be able to parse both the CEL and the CDF just as for any regular chip type. This are just the first few baby-step thoughts, but it is possible that this chip type could be brought into the Aroma framework with some work. /Henrik On Thu, Nov 12, 2015 at 12:33 AM, Michael Baudis wrote: > This doesn't sound good. It makes Oncoscan unusable for research projects. > > Michael. > > On 11 Nov 2015, at 23:40, Keith C wrote: > > From what I understand, the OncoScan assay has a different capture method > but in the end still involves hybridization to probes on a chip. > The output is two CEL files, A and C which represent AT and GC. Using their > oncoscan software, it combines the two CEL files into a .OSCHP file > which you can process with DNA Nexus. One advantage is that they have > precharacterized normal diploid cells so that a hapmap reference sample is > no longer required. However, the process is a pain and involves a lot of > manual interface clicking, file matching, and manual generation of images. > I have not found a way to simply export the segmentation data. I was told > by Affy that OncoScan does not use a CDF file, but rather a PGR.CLF file. > I'm trying > to get a hold of one to see what the difference is and if its convertable > into CDF format. > > What I mainly want is a chromosome explorer type output of > 1. images of all chromosomes for all samples. (that's 24 plots by hand per > sample using Nexus ) > 2. segmentation file including non-cnv altered segments. Currently Nexus > only outputs regions of significance. > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to a topic in the > Google Groups "aroma.affymetrix" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/aroma-affymetrix/Wez3wL1abiA/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[aroma.affymetrix] aroma.affymetrix v2.14.0 released
Hi,
aroma.affymetrix v2.14.0 (and friends) has been released and is now
available on CRAN for all the major operating systems. Install/update
by:
source("http://callr.org/install#aroma.affymetrix";)
This will take care of all dependencies and recommended packages as
well (also those hosted on Bioconductor and elsewhere).
What's new?
* This round of updates contains mostly bug fixes and robustness
improvements (== you spend less time troubleshooting and more time
doing science). For full details on what's updated, see below.
* If you're using PSCBS for segmentation or aroma.light for TumorBoost
normalization, please not that argument 'preserveScale' for
segmentByPairedPSCBS() / normalizeTumorBoost() now defaults to FALSE.
The transition from using TRUE (to FALSE) as the default started in
March 2014 and is now complete.
Cheers,
Henrik
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Updates to aroma.affymetrix
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Version: 2.14.0 [2015-10-24]
o AvgPlm, used by for instance doCRMAv2(), would give harmless warning
"Argument 'centers' for matrixStats::rowMads() has been renamed to
'center'. Please update code accordingly."
o ROBUSTNESS: Explicitly importing core R functions.
o CLEANUP: Removed methods marked as defunct in v2.11.3 (Feb 2014).
o ROBUSTNESS: fitCnProbes() for UnitModel could in rare cases give an
error on one of the internal sanity checks.
o BUG FIX: extractAlleleSet() for SnpChipEffectSet now needs to
load namspace 'oligoClasses' explicitly.
o BUG FIX: writeCdf() for AffyGenePDInfo gave "Error in
affxparser::writeCdf(...) : unused argument (pathname = ..." due to
a bug/typo introduced in 2.13.2. Thanks to Guillaume Devailly for
reporting on this.
Version: 2.13.2 [2015-05-26]
o ROBUSTNESS: Many functions now assert that they don't return file
data sets with duplicated entries.
o ROBUSTNESS: Package now declares all S3 methods.
o Package now requires R (>= 3.1.1) released July 2014. This allows
us to use BioC (>= 3.0) (October 2014).
Version: 2.13.1 [2015-01-23]
o Now a pre-existing monocell CDF can be recreated and overwritten
using getMonocellCdf(cdf, force=TRUE).
o BUG FIX: getMonocellCdf() for AffymetrixCdfFile would throw
"Error in (...) : 3 arguments passed to '(' which requires 1".
This was due to a typo (erroneous newline) introduced in 2.13.0.
Add package tests for this. Thanks to Qingzhou Zhang for reporting
on this.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Updates to aroma.core
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Version: 2.14.0 [2015-10-20]
o ROBUSTNESS: Explicitly importing core R functions.
o CLEANUP: Renamed apply() for SampleAnnotationFile to applyTo().
o CLEANUP: One rowMads(..., centers) to rowMads(..., center).
o CLEANUP: Drop prototype code never used.
o CLEANUP: Deprecated internal whatDataType() method.
o CLEANUP: Defuncted previously deprecated methods: nbrOfArrays() for
readData() for AromaMicroarrayDataSetTuple, AromaMicroarrayDataSet and
AromaUnitTotalCnBinarySet, as well as readData() for SampleAnnotationFile.
o CLEANUP: Removed previously (Feb 2014) defunct method patchPackage()
and patch().
o BUG FIX: writeRegions(..., format="wig") gave an error.
Version: 2.13.1 [2015-05-25]
o Package now requires R (>= 3.1.1) released July 2014. This allows us
to use BioC (>= 3.0) (October 2014).
o Relaxed sanity checks; now it's possible to allocate Aroma tabular
binary files with 200e6 rows (was 100e6 rows).
o getOutputDataSet() for AromaTransform gives more informative error
messages.
o ROBUSTNESS: exportAromaUnitPscnBinarySet() asserts that no
duplicated files are returned.
o ROBUSTNESS: Package now declares all S3 methods.
o BUG FIX: getOutputDataSet() for AromaTransform would sometimes given
an error due to the same output file being identified more than
once, for instance, when the full name of an output file is also
the prefix of another file. Thanks to Benilton Carvalho (Universidade
Estadual de Campinas, Sao Paulo, Brazil) for reporting on this.
o BUG FIX: extractRawMirroredAlleleBFractions() for RawAlleleBFractions
gave "Error in setSignals(res, dh) : object 'res' not found".
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Updates to R.filesets
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Version: 2.9.0 [2015-10-20]
o Add support for dsApply(..., .parallel="future"), which utilizes
the future package.
o CLEANUP: Defunct methods dropped.
o Package now requires R (>= 3.1.1) released July 2014. This allows
us to use BioC (>= 3.0) (October 2014).
Version: 2.8.0 [2015-08-06]
o Added support for sortBy(..., by="mixedroman") for GenericDataFileSet.
o Now commentChar="" and commentChar=FALSE also disables searching for
comment characters (just as commentChar=NULL) for TabularTextFile.
o Explicit import of 'utils' fun
Re: [aroma.affymetrix] Re: Affymetrix Oncoscan library files
I don't know anything about the OncoScan assay, but from looking at http://www.affymetrix.com/catalog/131419/AFFY/OncoScan%26%23174%3B+FFPE+Assay+Kit#1_3 it doesn't look like it's a classical Affymetrix chip. Basically, if CEL files are not produced, then Aroma almost certainly won't be able to process the data. Also, almost everything in Aroma requires a CDF, so unless a CDF can be obtained or created, that is also a show stopped. My $.02 /Henrik On Tue, Oct 20, 2015 at 2:16 PM, Keith C wrote: > Hi, > > did you ever figure out how to process Oncoscan arrays using aroma? > > thanks, > > -keith > > > On Monday, September 15, 2014 at 4:11:50 AM UTC-7, mbaudis wrote: >> >> Hi, >> >> has anybody processed Affymetrix Oncoscan arrays in aroma, and has >> generated the relevant CDF ... files? >> >> http://www.affymetrix.com/catalog/131419/AFFY/OncoScan+FFPE+Assay+Kit#1_3 >> >> >> Thanks, >> >> Michael. > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] "How to: Create a CDF file from Bioconductor Platform Design (PD) Info package" is miserably failing
Hi,
thank you. I can reproduce this. Explanation and fix below.
On Fri, Aug 14, 2015 at 5:27 PM, Guillaume Devailly wrote:
> Hi,
>
> I was trying to run this :
> http://www.aroma-project.org/howtos/createCdfFromBioconductorPlatformDesignInfo/
> to create a mighty cdf file for HuGene-2_0-st affymetrix array from this
> bioconductor annotation package.
>
> When running the example code (after installing the appropriate packages) :
>
> library("aroma.affymetrix")
> library("pd.hugene.1.0.st.v1")
> pathname <- writeCdf(pd.hugene.1.0.st.v1, tags =
> "pd.hugene.1.0.st.v1,HB20110111", overwrite = TRUE)
>
> I obtained this error:
>> pathname <- writeCdf(pd.hugene.1.0.st.v1,
>> tags="pd.hugene.1.0.st.v1,HB20110111", overwrite=TRUE)
> Loading required namespace: pdInfoBuilder
> Generating CDF file from Platform Design (PD) package...
> Platform Design (PD) package: pd.hugene.1.0.st.v1
> Output path: annotationData/chipTypes/HuGene-1_0-st-v1
> Filename: HuGene-1_0-st-v1,pd.hugene.1.0.st.v1,HB20110111.cdf
> Pathname to generated CDF:
> annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,pd.hugene.1.0.st.v1,HB20110111.cdf
> Chip type: HuGene-1_0-st-v1
> Tags: pd.hugene.1.0.st.v1,HB20110111
> Chip type dimensions: 1050x1050
> Total number of cells (probes): 1102500
> Querying Platform Design database...
> Units by: transcript
> Names by: fsetid
> Available database tables:
> [1] "chrom_dict" "core_mps" "featureSet" "level_dict" "pmfeature"
> [6] "table_info" "type_dict"
> SQL query:
>
> SELECT DISTINCT
> -- fid,
> meta_fsetid AS probeset_id,
> atom,
> x,
> y
> FROM pmfeature
> INNER JOIN core_mps USING(fsetid)
> ORDER BY probeset_id, atom
>
> 'data.frame': 861493 obs. of 4 variables:
>$ probeset_id: int 7892501 7892501 7892501 7892501 7892502 7892502
> 7892502 7892502 7892503 7892503 ...
>$ atom : int 1 2 3 5 7 10 11 12 13 14 ...
>$ x : int 870 28 638 888 108 411 918 958 928 495 ...
>$ y : int 110 899 469 863 984 622 657 949 361 447 ...
> 'data.frame': 861493 obs. of 4 variables:
>$ probeset_id: int 7892501 7892501 7892501 7892501 7892502 7892502
> 7892502 7892502 7892503 7892503 ...
>$ atom : int 1 2 3 5 7 10 11 12 13 14 ...
>$ x : int 870 28 638 888 108 411 918 958 928 495 ...
>$ y : int 110 899 469 863 984 622 657 949 361 447 ...
> Number of cells (probes) in PD database: 861493 (78.14%) of 1102500
> Querying Platform Design database...done
> Number of units: 33297
> Unit names: 7892501, 7892502, 7892503, ..., 8180418
> Average number of cells per units: 25.87
> List of 3
> $ 7892501:'data.frame': 4 obs. of 4 variables:
>..$ probeset_id: int [1:4] 7892501 7892501 7892501 7892501
>..$ atom : int [1:4] 1 2 3 5
>..$ x : int [1:4] 870 28 638 888
>..$ y : int [1:4] 110 899 469 863
> $ 7892502:'data.frame': 4 obs. of 4 variables:
>..$ probeset_id: int [1:4] 7892502 7892502 7892502 7892502
>..$ atom : int [1:4] 7 10 11 12
>..$ x : int [1:4] 108 411 918 958
>..$ y : int [1:4] 984 622 657 949
> $ 7892503:'data.frame': 4 obs. of 4 variables:
>..$ probeset_id: int [1:4] 7892503 7892503 7892503 7892503
>..$ atom : int [1:4] 13 14 17 18
>..$ x : int [1:4] 928 495 316 840
>..$ y : int [1:4] 361 447 686 698
> Error in affxparser::writeCdf(...) :
> unused argument (pathname =
> "annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,pd.hugene.1.0.st.v1,HB20110111.cdf")
>
>
> I am a simple R user and not an advanced package-maker wizard, so what I
> will say next is likely to be absurd, but:
>
> 1) AffyGenePDInfo.writeCdf.R source code:
> setMethodS3("writeCdf", "AffyGenePDInfo", function(this, tags=c("*"),
> unitsBy=c("transcript", "exon"), namesBy=c("fsetid", "id"), path=NULL,
> overwrite=FALSE, verbose=TRUE, ...) {
> [...]
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Writing CDF file
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> pathname <- .writeCdf(ffs, pathname=pathname, overwrite=overwrite,
> verbose=less(verbose));
> [...]
> }
>
> setMethodS3("writeCdf", "PDInfoList", function(ffs, pathname,
> overwrite=FALSE, ..., verbose=TRUE) {
> [...]
> pathnameT <- pushTemporaryFile(pathname, verbose=verbose);
>
> .writeCdf(pathnameT, cdfheader=cdfHeader, cdf=cdfList,
> cdfqc=NULL, verbose=verbose, overwrite=overwrite);
> [...]
> }
> I am totaly confused by what is this .writeCdf function. Is it the writeCdf
> function from affxparser package?
>
> 2) affxparser::writeCdf first parameter is fname and not pathname. Hence the
> error?
> writeCdf(fname, cdfheader, cdf, cdfqc, overwrite=FALSE, verbose=0)
You did a pretty good job nailing this one down. The .writeCdf() is a
light-weig
Re: [aroma.affymetrix] Filtering in FIRMA
Hi, the fit() method [http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis/] takes argument 'units', which effectively defaults to units = seq_len(nbrOfUnits(cdf)). If you wish to fit only a subset of the units, you can do something like fit(plm, units=c(10:50, 540:800)) If you're using doFIRMA(), it is unfortunately not possible to specify 'units' this way. Hope this helps Henrik On Wed, Aug 12, 2015 at 2:25 PM, Marijke Van Moerbeke wrote: > Hi > > I noticed that the FIRMA procedure is implemented to work on the raw .CEL > files. > Is there a way to select only a specific set of units (By this I mean exons) > on which FIRMA needs to be performed? And by this to leave out units that > are for example not informative? > > Thanks! > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] Getting error with AffymetrixCdfFile$fromChipType command
You probably meant:
cdf <- AffymetrixCdfFile$byChipType("HG_U95Av2")
The fromChipType() method was deprecated a long time ago and
eventually also removed.
/Henrik
On Wed, Jun 10, 2015 at 2:54 PM, anarayan wrote:
> Hi,
>
> I am getting the error: Error: attempt to apply non-function when I run the
> command: cdf <- AffymetrixCdfFile$fromChipType("HG_U95Av2"). Not sure what
> is going on. The command was working about an hour ago but it is now giving
> me this error.
>
> Thanks
>
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> ---
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to aroma-affymetrix+unsubscr...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
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Re: [aroma.affymetrix] doCRMAv2 vs individual normalization steps
Yes, you can use the CRMA v2 methods instead of the CRMA v1 method for these older chip types as well. The only difference is that CRMA v2 was optimized (=optimized signal-to-noise ratios) only for GenomeWideSNP_5 and forward, but all practical purposes you can use CRMA v2 for your needs. I do this myself. So, yes, run doCRMAv2(). /Henrik On Tue, Jun 9, 2015 at 9:20 AM, Arshi Arora wrote: > > Hi Henrik, > > I have paired normal tumor files from chip type Mapping250K_Nsp > I am following two vignettes - > http://www.aroma-project.org/vignettes/PairedPSCBS-lowlevel/ > > Vignette: Paired parent-specific copy-number segmentation > > and > > http://www.aroma-project.org/vignettes/CRMAv1/ > > Total copy number analysis using CRMA v1 (10K, 100K, 500K) > > > I want to get the copy number of each SNP, so I want - > > ## NA06985 NA06991 NA06993 NA06994 NA07000 NA07019 > ## SNP_A-1938296 -0.0402 0.0391 -0.0518 -0.0414 0.1967 0.0476 > ## SNP_A-4259059 0.1519 -0.1174 0.2330 -0.1432 -0.2650 0.1086 > ## SNP_A-1939610 -0.4355 -0.3506 -0.0181 0.0179 0.3192 0.2245 > > http://www.aroma-project.org/vignettes/calculating_raw_total_copy_numbers_manually/ > h > > Calculating raw total copy numbers manually. This vignette tells us to > follow vignette - Total copy number analysis using CRMA v1 (10K, 100K, > 500K). In this vignette I am doing the normalizing steps individually. > > > My question is - > Instead of doing correction of allelic crosstalk, quantile normalization, > and fragment normalization can I just do doCRMAv2 for each pair and get its > CnChipSizeEffect and then go to the vignette of calculating raw total copy > numbers manually? > > I also want the BAF of these samples and I feel as if I am basically > repeating normalizing step in order to get these 2 tasks. > > I have some 150 arrays. > > Thanks, > Arshi > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] Changing the Aroma settings (RMA MedianPolish threshold ) in the latest version of the aroma.affymetrix
s(cs)
> cls <- 1:length(nm)
>
> cat("Extracting standardized residuals.\n")
>
> rsu1 <- lapply(rsu,FUN=function(u,cls) {
> r <- log2(u[[1]]$eps)
> m <- mad(r)
> calcMeans(r/m,cls)
> },cls=cls)
> nProbe <- sapply(rsu,FUN=function(u) nrow(u[[1]]$eps))
>
> rm(rsu)
> gco <- gc()
>
>
> upLimit <- 3485 # the length of unit with maximum number of probes
> w <- (nProbe >= minProbes) & (nProbe <= upLimit)
> nProbe <- nProbe[w]
>
> mufScores <- t(sapply( rsu1[w], FUN=function(u) mufColumns(u)))
>
> The session info is:
>
> R version 3.1.2 (2014-10-31)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] stringr_1.0.0 statmod_1.4.21 limma_3.22.7
> fdrtool_1.2.14 FIRMAGene_0.9.8 aroma.light_2.2.1
> aroma.affymetrix_2.13.1 aroma.core_2.13.0 R.devices_2.13.0
> R.filesets_2.7.1R.utils_2.0.2
> [12] R.oo_1.19.0 R.methodsS3_1.7.0 affxparser_1.38.0
>
> loaded via a namespace (and not attached):
> [1] aroma.apd_0.6.0base64enc_0.1-3digest_0.6.8 DNAcopy_1.40.0
> magrittr_1.5 matrixStats_0.14.0 PSCBS_0.44.0 R.cache_0.11.0
> R.huge_0.9.0 R.rsp_0.20.0 stringi_0.4-1 tools_3.1.2
>
> Regards,
> S
>
>
> On Thursday, June 4, 2015 at 5:31:46 PM UTC+1, Henrik Bengtsson wrote:
>>
>> Hi,
>>
>> could you please share the exact calls you are using and elaborate a
>> bit more what makes you think it's not working? That'll help me help
>> you.
>>
>> Henrik
>>
>> On Thu, Jun 4, 2015 at 6:40 AM, sanjana wrote:
>> > Hi,
>> >
>> > Our group is working with HTA platform and using aroma.affymetrix for
>> > the
>> > analysis. We intend to change the RMA median polish threshold in aroma
>> > settings. We are able to achieve this in version 2.13.1 but somehow not
>> > in
>> > version 2.13.2?
>> >
>> > Has anyone else experienced the same thing? Is it possible there is a
>> > bug
>> > in the 2.13.2 version?
>> >
>> > Thanks,
>> >
>> > --
>> > --
>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> > latest
>> > version of the package, 2) to report the output of sessionInfo() and
>> > traceback(), and 3) to post a complete code example.
>> >
>> >
>> > You received this message because you are subscribed to the Google
>> > Groups
>> > "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> > To post to this group, send email to aroma-af...@googlegroups.com
>> > To unsubscribe and other options, go to
>> > http://www.aroma-project.org/forum/
>> >
>> > ---
>> > You received this message because you are subscribed to the Google
>> > Groups
>> > "aroma.affymetrix" group.
>> > To unsubscribe from this group and stop receiving emails from it, send
>> > an
>> > email to aroma-affymetr...@googlegroups.com.
>> > For more options, visit https://groups.google.com/d/optout.
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> ---
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to aroma-affymetrix+unsubscr...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
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Re: [aroma.affymetrix] Changing the Aroma settings (RMA MedianPolish threshold ) in the latest version of the aroma.affymetrix
Hi, could you please share the exact calls you are using and elaborate a bit more what makes you think it's not working? That'll help me help you. Henrik On Thu, Jun 4, 2015 at 6:40 AM, sanjana wrote: > Hi, > > Our group is working with HTA platform and using aroma.affymetrix for the > analysis. We intend to change the RMA median polish threshold in aroma > settings. We are able to achieve this in version 2.13.1 but somehow not in > version 2.13.2? > > Has anyone else experienced the same thing? Is it possible there is a bug > in the 2.13.2 version? > > Thanks, > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] cfit error while doCRMAv2
On Mon, Jun 1, 2015 at 9:17 AM, Arshi Arora wrote:
> I was able to get the plot. But I reinstalled sfit anyways and it works now!
> Thanks so much Henrik.
Great to hear.
> I get a lot of these warnings after running - any advice ?
>
> Argument 'centers' for matrixStats::rowMads() has been renamed to 'center'.
> Please update code accordingly.
This is a harmless _warning_ that you can happily ignore. (I actually
fixed this only a few minutes ago so you won't see it in future
versions, cf. https://goo.gl/PMLv0a - but it will take a while before
you see the update on CRAN).
>
> I also get this warning at cbs stage.
> In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome, data.type =
> "logratio", :
> array has repeated maploc positions
That is also a harmless warnings created by the DNAcopy implementation
of CBS - it happens when two CN probes on the array happens to have
the exact same genomic location. This is a warning I cannot do
anything about, but again, it's harmless.
Henrik
>
> Thanks so much!
> Arshi
>
> On Friday, May 29, 2015 at 7:35:13 PM UTC-4, Henrik Bengtsson wrote:
>>
>> BTW,
>>
>> the output of
>>
>> packageDescription("sfit")
>>
>> is also useful for troubleshooting - it will particularly tell you
>> when and for what version of R it was build and installed.
>>
>> /Henrik
>>
>> On Fri, May 29, 2015 at 4:33 PM, Henrik Bengtsson
>> wrote:
>> > This all looks good, so it's indeed a weird error that I most likely
>> > think is due to some hiccups when the 'sfit' package was installed
>> > (which defines the cfit() function).
>> >
>> > For troubleshooting, first try:
>> >
>> > url <-
>> > "https://raw.githubusercontent.com/HenrikBengtsson/aroma.core/develop/tests/fitGenotypeCone.R";
>> > source(url)
>> >
>> > You should get a plot similar to the one in the attached PNG. If
>> > you're R installation does not support "https" (started to be
>> > optionally supported in R 3.2.0), the you can run the above script as
>> >
>> > url <-
>> > "https://raw.githubusercontent.com/HenrikBengtsson/aroma.core/develop/tests/fitGenotypeCone.R";
>> > pathname <- R.utils::downloadFile(url)
>> > source(pathname)
>> >
>> > instead.
>> >
>> > If you get the error here, we have a minimal reproducible example for
>> > your problem (without the need of Affymetrix data etc). If you get
>> > the error, try to reinstall 'sfit' - in a fresh R session - as:
>> >
>> > source("http://callr.org/install#sfit[!]";)
>> >
>> > Note the exclamation mark - it forces installation even if you already
>> > got the latest version.
>> >
>> > After this, retry the above again. Did the problem go away?
>> >
>> > /Henrik
>> >
>> >
>> > On Fri, May 29, 2015 at 12:22 PM, arshi wrote:
>> >> Sorry about not posting that.
>> >>
>> >>> sessionInfo()
>> >> R version 3.2.0 (2015-04-16)
>> >> Platform: x86_64-pc-linux-gnu (64-bit)
>> >> Running under: Ubuntu 14.04.2 LTS
>> >>
>> >> locale:
>> >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> >> [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>> >> [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>> >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> >> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>> >>
>> >> attached base packages:
>> >> [1] stats graphics grDevices utils datasets methods base
>> >>
>> >> other attached packages:
>> >> [1] GLAD_2.32.0 RColorBrewer_1.1-2 R.rsp_0.20.0
>> >> [4] DNAcopy_1.42.0 sfit_0.3.0 aroma.light_2.4.0
>> >> [7] aroma.affymetrix_2.13.1 aroma.core_2.13.0 R.devices_2.13.0
>> >> [10] R.filesets_2.7.1R.utils_2.0.2 R.oo_1.19.0
>> >> [13] affxparser_1.40.0 R.methodsS3_1.7.0
>> >>
>> >> loaded via a namespace (and not attached):
>> >> [1] matrixStats_0.14.0 digest_0.6.8 R.huge_0.9.0
>> >> PSCBS_0.44.0
>> >> [5] splines_3.2.0 tools_3.2.0R.cache_0.10.0
>> >> base64enc_0.1-2
>> >> [9] aroma.apd_0.6.0tcltk_3.2.0
>> >>
>
Re: [aroma.affymetrix] cfit error while doCRMAv2
BTW,
the output of
packageDescription("sfit")
is also useful for troubleshooting - it will particularly tell you
when and for what version of R it was build and installed.
/Henrik
On Fri, May 29, 2015 at 4:33 PM, Henrik Bengtsson
wrote:
> This all looks good, so it's indeed a weird error that I most likely
> think is due to some hiccups when the 'sfit' package was installed
> (which defines the cfit() function).
>
> For troubleshooting, first try:
>
> url <-
> "https://raw.githubusercontent.com/HenrikBengtsson/aroma.core/develop/tests/fitGenotypeCone.R";
> source(url)
>
> You should get a plot similar to the one in the attached PNG. If
> you're R installation does not support "https" (started to be
> optionally supported in R 3.2.0), the you can run the above script as
>
> url <-
> "https://raw.githubusercontent.com/HenrikBengtsson/aroma.core/develop/tests/fitGenotypeCone.R";
> pathname <- R.utils::downloadFile(url)
> source(pathname)
>
> instead.
>
> If you get the error here, we have a minimal reproducible example for
> your problem (without the need of Affymetrix data etc). If you get
> the error, try to reinstall 'sfit' - in a fresh R session - as:
>
> source("http://callr.org/install#sfit[!]";)
>
> Note the exclamation mark - it forces installation even if you already
> got the latest version.
>
> After this, retry the above again. Did the problem go away?
>
> /Henrik
>
>
> On Fri, May 29, 2015 at 12:22 PM, arshi wrote:
>> Sorry about not posting that.
>>
>>> sessionInfo()
>> R version 3.2.0 (2015-04-16)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 14.04.2 LTS
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] GLAD_2.32.0 RColorBrewer_1.1-2 R.rsp_0.20.0
>> [4] DNAcopy_1.42.0 sfit_0.3.0 aroma.light_2.4.0
>> [7] aroma.affymetrix_2.13.1 aroma.core_2.13.0 R.devices_2.13.0
>> [10] R.filesets_2.7.1R.utils_2.0.2 R.oo_1.19.0
>> [13] affxparser_1.40.0 R.methodsS3_1.7.0
>>
>> loaded via a namespace (and not attached):
>> [1] matrixStats_0.14.0 digest_0.6.8 R.huge_0.9.0 PSCBS_0.44.0
>> [5] splines_3.2.0 tools_3.2.0R.cache_0.10.0
>> base64enc_0.1-2
>> [9] aroma.apd_0.6.0tcltk_3.2.0
>>
>>
>> On Friday, May 29, 2015 at 3:17:18 PM UTC-4, Henrik Bengtsson wrote:
>>>
>>> First of all, what versions of packages do you have, e.g. what's the
>>> output sessionInfo() after doing:
>>>
>>> library("aroma.affymetrix")
>>> library("sfit")
>>> sessionInfo()
>>>
>>>
>>> /Henrik
>>>
>>> On Fri, May 29, 2015 at 9:51 AM, arshi wrote:
>>> > Hi, I am following the vignette on paired total copy number analysis.
>>> >
>>> > So far, my cdf files and the rawData directory structure looks ok. When
>>> > I do
>>> > dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE,
>>> > verbose=verbose)
>>> > I get the following error and I can't see a dsList object created.
>>> > Error in UseMethod("cfit") :
>>> > no applicable method for 'cfit' applied to an object of class
>>> > "c('matrix',
>>> > 'double', 'numeric')"
>>> >
>>> > I am also pasting the rest of the verbose output. The error is at the
>>> > bottom
>>> > of the output. Thanks for your help!
>>> >
>>> > CRMAv2...
>>> > CRMAv2/Setting up CEL set...
>>> >AffymetrixCelSet:
>>> >Name: data_aroma
>>> >Tags:
>>> >Path: rawData/data_aroma/Mapping250K_Nsp
>>> >Platform: Affymetrix
>>> >Chip type: Mapping250K_Nsp
>>> >Number of arrays: 4
>>> >Names: RCC, RCC, RCC, RCC
Re: [aroma.affymetrix] cfit error while doCRMAv2
This all looks good, so it's indeed a weird error that I most likely
think is due to some hiccups when the 'sfit' package was installed
(which defines the cfit() function).
For troubleshooting, first try:
url <-
"https://raw.githubusercontent.com/HenrikBengtsson/aroma.core/develop/tests/fitGenotypeCone.R";
source(url)
You should get a plot similar to the one in the attached PNG. If
you're R installation does not support "https" (started to be
optionally supported in R 3.2.0), the you can run the above script as
url <-
"https://raw.githubusercontent.com/HenrikBengtsson/aroma.core/develop/tests/fitGenotypeCone.R";
pathname <- R.utils::downloadFile(url)
source(pathname)
instead.
If you get the error here, we have a minimal reproducible example for
your problem (without the need of Affymetrix data etc). If you get
the error, try to reinstall 'sfit' - in a fresh R session - as:
source("http://callr.org/install#sfit[!]";)
Note the exclamation mark - it forces installation even if you already
got the latest version.
After this, retry the above again. Did the problem go away?
/Henrik
On Fri, May 29, 2015 at 12:22 PM, arshi wrote:
> Sorry about not posting that.
>
>> sessionInfo()
> R version 3.2.0 (2015-04-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 14.04.2 LTS
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] GLAD_2.32.0 RColorBrewer_1.1-2 R.rsp_0.20.0
> [4] DNAcopy_1.42.0 sfit_0.3.0 aroma.light_2.4.0
> [7] aroma.affymetrix_2.13.1 aroma.core_2.13.0 R.devices_2.13.0
> [10] R.filesets_2.7.1R.utils_2.0.2 R.oo_1.19.0
> [13] affxparser_1.40.0 R.methodsS3_1.7.0
>
> loaded via a namespace (and not attached):
> [1] matrixStats_0.14.0 digest_0.6.8 R.huge_0.9.0 PSCBS_0.44.0
> [5] splines_3.2.0 tools_3.2.0R.cache_0.10.0
> base64enc_0.1-2
> [9] aroma.apd_0.6.0tcltk_3.2.0
>
>
> On Friday, May 29, 2015 at 3:17:18 PM UTC-4, Henrik Bengtsson wrote:
>>
>> First of all, what versions of packages do you have, e.g. what's the
>> output sessionInfo() after doing:
>>
>> library("aroma.affymetrix")
>> library("sfit")
>> sessionInfo()
>>
>>
>> /Henrik
>>
>> On Fri, May 29, 2015 at 9:51 AM, arshi wrote:
>> > Hi, I am following the vignette on paired total copy number analysis.
>> >
>> > So far, my cdf files and the rawData directory structure looks ok. When
>> > I do
>> > dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE,
>> > verbose=verbose)
>> > I get the following error and I can't see a dsList object created.
>> > Error in UseMethod("cfit") :
>> > no applicable method for 'cfit' applied to an object of class
>> > "c('matrix',
>> > 'double', 'numeric')"
>> >
>> > I am also pasting the rest of the verbose output. The error is at the
>> > bottom
>> > of the output. Thanks for your help!
>> >
>> > CRMAv2...
>> > CRMAv2/Setting up CEL set...
>> >AffymetrixCelSet:
>> >Name: data_aroma
>> >Tags:
>> >Path: rawData/data_aroma/Mapping250K_Nsp
>> >Platform: Affymetrix
>> >Chip type: Mapping250K_Nsp
>> >Number of arrays: 4
>> >Names: RCC, RCC, RCC, RCC [4]
>> >Time period: 2010-06-29 12:49:28 -- 2010-11-27 00:08:30
>> >Total file size: 250.45MB
>> >RAM: 0.01MB
>> > CRMAv2/Setting up CEL set...done
>> > CRMAv2...
>> >Arguments:
>> >combineAlleles: FALSE
>> >arrays:
>> > chr ""
>> >Data set
>> >AffymetrixCelSet:
>> >Name: data_aroma
>> >Tags:
>> >Path: rawData/data_aroma/Mapping250K_Nsp
>> >Platf
Re: [aroma.affymetrix] extract LRR and BAF from ACNE results
So, there are few things here:
1. In the Aroma Framework, we always try to store estimates/signals on
the "original" scale, e.g. even if, say, chip-effect estimates are
original on the log scale, we unlog those before saving. That is a
policy with the rationale that all data can always be represented on
the "original" scale but not always on, say, the log scale. An
example of the latter is when a probe signal ends up being slightly
negative after calibration and normalization. If that would have been
stored on the log-scale we would have lost the information, i.e. it
would be stored as NaN. Same problem with a signal that is exactly
zero (-Inf on the log scale). Why bother? For instance, say you end
up with replicated probe signals for a single SNP where they all
fluctuate around zero. After averaging, the average signal may end up
non-negative. If we stored on the log scale the averaging would have
only been on the signals that were positive (because we lost the
non-positive one). So, that's that rational.
2. For methods estimating "CNs" it depends on their approach/method/design:
(a) For instance, the CRMA v1 and CRMA v2 methods (ours; happens to be
implemented in the Aroma Framework, but should never be referred to as
the "Aroma CN method", "aroma.affymetrix CN method" or similar), we
end up with "CN signals" that have not yet been standardized relative
to a reference. In other words, those signals are "all over the
place", because each of them are scaled with an unknown scale factors.
It is only when you have a reference when you can create "CN
ratios", e.g. C = tumor / matched normal or C = sample / pooled
average, etc. Comment: For CRMA v2, this is not that surprising,
because that method was specifically designed to work for each array
independently. That means you get "CN signals" out from a single
array, but then you need to compare them to a reference.
(b) The ACNE method (however), calculates CN ratios for you. This is
by design of the model, simply because how the NMF factorization model
works, cf. Eqns (10)-(14) in
http://bioinformatics.oxfordjournals.org/content/26/15/1827.full.
Comment: The ACNE method is a multi-array method requiring many arrays
to work and borrows information across arrays (e.g. estimate SNP
effects). Since this information is already done, it can equally well
return CN ratios for you. Having said this, there is nothing
preventing you from taking the ratios relative to another reference
(ratio), e.g. effectively C = (T / R) / (R / R*) = T / R.
So, in the ACNE vignette
[http://www.aroma-project.org/vignettes/ACNE/] that you're following
there is, near the end:
cf <- ces[[1]]
data <- extractTotalAndFreqB(cf, units=units)
CT <- data[,"total"]
Since you used ACNE to estimate the CNs, here 'CT' is indeed a "CN
ratios". The reason why we still refer to it as a "total" signal, is
because that is the most generic name we could come up with for the
underlying file format.
Hope this clarifies
/Henrik
On Fri, May 29, 2015 at 6:52 AM, hongen xu wrote:
> Dear Aroma.affymetrix teem,
>
> I followed the vignette "Allele-specific copy numbers using non-negative
> matrix factorization". I want to extract LRR and BAF to feed into another
> software "ASCAT" to correct aneuploidy and normal contamination.
>
> From the vignette, I can use extractTotalAndFreqB to extract total CN and
> BAF. My question is how can I get LRR from Total CN. I went through this
> thread "creat binary data files containing BAF data", but get confused.
>
> quote from "creat binary data files containing BAF data"
> "The take-home message is that
> the definition of "log2 ratios" has become de facto standard in our
> field, where as "CN" is a bit ambiguous, and can mean "CN ratio"
> (C=theta/thetaR, or C=2*theta/thetaR) as well as "CN intensity"
> (theta). By adding tags we try to make this less ambiguous."
>
> How total CN was defined in aroma.affymetrix?
>
>
> Best regards,
> Hongen
>
>
>
>
>
>
>
>
> my code
>
>
> library("aroma.affymetrix")
> library("ACNE")
>
>
> log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> # Don't display too many decimals.
> options(digits=4)
>
>
> #Verifying annotation data files
> cdf <- AffymetrixCdfFile$byChipType("CytoScanHD_Array");
> print(cdf)
> gi <- getGenomeInformation(cdf)
> print(gi)
> si <- getSnpInformation(cdf)
> print(si)
> acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
> print(acs)
>
> ##raw data sets
> csR<- AffymetrixCelSet$byName("smida", cdf=cdf);
>
> ###step 1 Calibration for crosstalk between allele probe pairs
> acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
>
> print(acc)
>
> csC <- process(acc, verbose=verbose)
> print(csC)
>
>
> ##Step 2 - Normalization for nucleotide-position probe sequence effects
> bpn <- BasePositionNormalization(csC, target="zero")
> csN <- process(bpn, verbose=verbose)
> cs <- csN
>
>
>
> #step 3
> #Probe summarization using non-negative-matrix factor
Re: [aroma.affymetrix] cfit error while doCRMAv2
First of all, what versions of packages do you have, e.g. what's the
output sessionInfo() after doing:
library("aroma.affymetrix")
library("sfit")
sessionInfo()
/Henrik
On Fri, May 29, 2015 at 9:51 AM, arshi wrote:
> Hi, I am following the vignette on paired total copy number analysis.
>
> So far, my cdf files and the rawData directory structure looks ok. When I do
> dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE, verbose=verbose)
> I get the following error and I can't see a dsList object created.
> Error in UseMethod("cfit") :
> no applicable method for 'cfit' applied to an object of class "c('matrix',
> 'double', 'numeric')"
>
> I am also pasting the rest of the verbose output. The error is at the bottom
> of the output. Thanks for your help!
>
> CRMAv2...
> CRMAv2/Setting up CEL set...
>AffymetrixCelSet:
>Name: data_aroma
>Tags:
>Path: rawData/data_aroma/Mapping250K_Nsp
>Platform: Affymetrix
>Chip type: Mapping250K_Nsp
>Number of arrays: 4
>Names: RCC, RCC, RCC, RCC [4]
>Time period: 2010-06-29 12:49:28 -- 2010-11-27 00:08:30
>Total file size: 250.45MB
>RAM: 0.01MB
> CRMAv2/Setting up CEL set...done
> CRMAv2...
>Arguments:
>combineAlleles: FALSE
>arrays:
> chr ""
>Data set
>AffymetrixCelSet:
>Name: data_aroma
>Tags:
>Path: rawData/data_aroma/Mapping250K_Nsp
>Platform: Affymetrix
>Chip type: Mapping250K_Nsp
>Number of arrays: 4
>Names: RCC, RCC, RCC, RCC [4]
>Time period: 2010-06-29 12:49:28 -- 2010-11-27 00:08:30
>Total file size: 250.45MB
>RAM: 0.01MB
>Checking whether final results are available or not...
>Checking whether final results are available or not...done
>CRMAv2/Allelic crosstalk calibration...
> AllelicCrosstalkCalibration:
> Data set: data_aroma
> Input tags:
> User tags: *
> Asterisk ('*') tags: ACC,-XY
> Output tags: ACC,-XY
> Number of files: 4 (250.45MB)
> Platform: Affymetrix
> Chip type: Mapping250K_Nsp
> Algorithm parameters: {rescaleBy: chr "groups", targetAvg:
> num [1:2] 2200 2200, subsetToAvg: int [1:6409592] 1 2 3 4 5 6 7 8 9 10 ...,
> mergeShifts: logi TRUE, B: int 1, flavor: chr "sfit",
> algorithmParameters:List of 3, ..$ alpha: num [1:8] 0.1 0.075 0.05 0.03 0.01
> 0.0025 0.001 0.0001, ..$ q: num 2, ..$ Q: num 98}
> Output path: probeData/data_aroma,ACC,-XY/Mapping250K_Nsp
> Is done: FALSE
> RAM: 24.46MB
> Calibrating data set for allelic cross talk...
> Compressing model parameter to a short format...
> Compressing model parameter to a short format...done
> Calibrating 4 arrays...
> Path: probeData/data_aroma,ACC,-XY/Mapping250K_Nsp
> Array #1 ('RCC') of 4...
>setsOfProbes:
>List of 2
> $ snps :List of 7
> ..$ A/C: int [1:129194, 1:2] 562 640260 6430798
> 890622 858750 4681948 347160 5718766 2746760 2790782 ...
> .. ..- attr(*, "dimnames")=List of 2
> .. .. ..$ : NULL
> .. .. ..$ : chr [1:2] "A" "C"
> ..$ A/G: int [1:51, 1:2] 4969704 4677672
> 4787718 5185370 1363100 4109892 1558340 1352256 1332280 4969616 ...
> .. ..- attr(*, "dimnames")=List of 2
> .. .. ..$ : NULL
> .. .. ..$ : chr [1:2] "A" "G"
> ..$ A/T: int [1:107590, 1:2] 1028670 3832004
> 5665036 1832744 4167500 4571986 4938090 747094 2207654 5855716 ...
> .. ..- attr(*, "dimnames")=List of 2
> .. .. ..$ : NULL
> .. .. ..$ : chr [1:2] "A" "T"
> ..$ C/G: int [1:156840, 1:2] 4747206 3909704
> 1725666 600232 416088 1138554 6393394 6389120 555046 2960654 ...
> .. ..- attr(*, "dimnames")=List of 2
> .. .. ..$ : NULL
> .. .. ..$ : chr [1:2] "C" "G"
> ..$ C/T: int [1:572339, 1:2] 3789122 5491344 768382
> 4974648 387402 2086744 1183506 5290380 6464728 6121838 ...
> .. ..- attr(*, "dimnames")=List of 2
> .. .. ..$ : NULL
> .. .. ..$ : chr [1:2] "C" "T"
> .
Re: [aroma.affymetrix] Adjusting for sample-specific median signal prior to segmentation
[Reposting from an approved email address]
Hi Benilton,
The locus level (total) CN ratios passed to CBS is simply the
log2(T/R), where 'T' is the total CN signal (no ratio) for sample T
("tumor" say) and 'R' is ditto for the reference used to standardize
(aka "normalize" by some books). Typically, 'R' is either a matched
normal or a global reference (e.g. median across all available 'T':s).
In the end of the day, if you see global biases in mean/median levels
after CBS, then that is already there in the log2(T/R) ratios, or
equivalently, in the T/R ratios. It's not clear what type of
reference 'R' you use, and what preprocessing, but the
genome-wide/global average - median(log2(T/R)) - is basically assumed
to be zero at the point you pass it to CBS.
>From your figure it also not clear what the scale of your color scale
is; could it be that threshold for "white" is so small that even the
teeniest bias in median(log2(T/R)) shows up? Looking the the
ChromosomeExplorer plots helps here.
You could extract the T's and R's manually and run it trough
DNAcopy::segment() (or PSCBS::segmentByCBS()) manually to see if you
can do a better centralization of the log2(T/R) signals.
Hope this helps
Henrik
On May 19, 2015 10:27 PM, "Benilton Carvalho"
wrote:
>
> Hi everyone,
>
> if you check the image at:
>
>
https://dl.dropboxusercontent.com/u/83643/Screen%20Shot%202015-05-20%20at%201.50.50%20AM.png
>
> you'll see segmentation results for a few human samples across multiple
chromosomes. This was achieved via CBS (under the aroma framework,
therefore CbsModel).
>
> A few samples show constant gain/loss levels across several chrs and
that's quite unlikely, suggesting the possibility of an issue with the
sample-specific intensity levels. My question: is there a simple solution
under the aroma framework to adjust for that?
>
> thanks, b
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the
latest version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
>
>
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>
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version of the package, 2) to report the output of sessionInfo() and
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Re: [aroma.affymetrix] Error when calling doCRMAv2
It's a known bug (due to a single newline added by mistake) in
aroma.affymetrix 2.13.0. Fixed in 2.13.1. Update by:
source('http://callr.org/install#aroma.affymetrix')
and you should be ready to go.
/Henrik
On Fri, Mar 13, 2015 at 11:35 AM, Georg wrote:
> Hi There,
>
> I am trying to use doCRMAv2 to smooth data. The command I used is like this:
>
> ces <- doCRMAv2(celFile, cdf=cdf, combineAlleles=FALSE, verbose=verbose)
>
> The command ran a while, the I got the message as this:
>
>
> Error in (...) : 3 arguments passed to '(' which requires 1
> Calls: doCRMAv2 ... createMonocellCdf.AffymetrixCdfFile -> .writeCdfUnits
> Execution halted
>
> I am using R 3.1.3. Any idea what I did wrong? Thanks.
>
> George
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> ---
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Re: [aroma.affymetrix] annotation file update
Hi. See Section 'Aroma-specific annotation files' at http://aroma-project.org/howtos/ for "how tos" on updating UGP and UFL. Those subpages have straightforward/detailed instructions how to import from NetAffx files. Please consider sharing your generated files; we're happy to host. Cheers, Henrik On Tue, Mar 10, 2015 at 5:53 AM, Francois wrote: > Hello Henrik, > > What fields should be updated in annotation files for SNP 500K from the > latest version supported by NetAffyx (GRCh37) to current version (GRCh38), > what columns exactly are used by the package for each annotation file? Would > updating genomic positions with latest dbSNP in the annot.csv and probe_tab > be sufficient? > > Thank you, > > François > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] Re: strange result from PSCBS
Could be a sample annotation mistake. Wouldn't be the first time it happened. On Thu, Mar 5, 2015, 01:34 Chengyu Liu wrote: > You might be right. The BAF of the normal sample is strange if the way I > check is correct. I checked the how many bands there are. Normally there > are three but there are only two bands in the normal sample(see > attachment). The tumor sample looks okey. > > > Br, > Chengyu > > > On Wednesday, February 25, 2015 at 10:36:10 PM UTC+2, Henrik Bengtsson > wrote: > >> Hi, it's not easy to say. My point is that you look at the normal >> data, i.e. BAF (but also TCN relative to a global reference), you may >> have more clues on the quality of the normal sample. If that is bad, >> then then tumor-normal TCN is most likely bad too. >> >> /Henrik >> >> On Tue, Feb 24, 2015 at 7:42 AM, Chengyu Liu >> wrote: >> > I understand DH is defined only for heterozygous SNPs. But the total >> copy >> > number estimates look ok. Do you think I need to discard this sample or >> not >> > when I do total copy number analysis? I will discard this sample when I >> do >> > parent-specific analysis. But not sure whether I should leave this >> sample >> > out for alteration calls. >> > >> > You are expert of PSCBS, can you give me suggestion here? >> > >> > Br, >> > C.Y >> > >> > On Monday, February 23, 2015 at 9:54:47 PM UTC+2, Henrik Bengtsson >> wrote: >> >> >> >> Hi, >> >> >> >> DH signals are only defined for heterozygous SNPs, so lack of DHs >> >> indicates a problem with the matched normal BAFs (see my other email). >> >> >> >> /Henrik >> >> >> >> On Mon, Feb 23, 2015 at 1:53 AM, Chengyu Liu >> wrote: >> >> > It is difficult for me to say whether it is failed or the normal >> sample >> >> > is >> >> > nose. Can you have a look at these four figures ? They are from two >> >> > paired >> >> > tumor samples. One of them is missing DH . In the other sample, >> minor cn >> >> > is >> >> > 0 and major cn is 1. I am also attaching the total copy number >> estimate. >> >> > >> >> > Br, >> >> > Chengyu >> >> > >> >> > On Wednesday, February 18, 2015 at 11:25:48 PM UTC+2, Henrik >> Bengtsson >> >> > wrote: >> >> >> >> >> >> DH is only defined from heterozygous SNPs. If you don't see any DH >> >> >> signals, that indicates that none of the SNPs where called >> >> >> heterozygous. This could be an indicatation of a failed or a very >> >> >> noise normal sample. >> >> >> >> >> >> /Henrik >> >> > >> >> > -- >> >> > -- >> >> > When reporting problems on aroma.affymetrix, make sure 1) to run the >> >> > latest >> >> > version of the package, 2) to report the output of sessionInfo() and >> >> > traceback(), and 3) to post a complete code example. >> >> > >> >> > >> >> > You received this message because you are subscribed to the Google >> >> > Groups >> >> > "aroma.affymetrix" group with website http://www.aroma-project.org/. >> >> >> > To post to this group, send email to aroma-af...@googlegroups.com >> >> > To unsubscribe and other options, go to >> >> > http://www.aroma-project.org/forum/ >> >> > >> >> > --- >> >> > You received this message because you are subscribed to the Google >> >> > Groups >> >> > "aroma.affymetrix" group. >> >> > To unsubscribe from this group and stop receiving emails from it, >> send >> >> > an >> >> > email to aroma-affymetr...@googlegroups.com. >> >> > For more options, visit https://groups.google.com/d/optout. >> > >> > -- >> > -- >> > When reporting problems on aroma.affymetrix, make sure 1) to run the >> latest >> > version of the package, 2) to report the output of sessionInfo() and >> > traceback(), and 3) to post a complete code example. >> > >> > >> > You received this message because you are subscribed to the Google >> Groups >> > "aroma.affymetrix" group with website http://www.
Re: [aroma.affymetrix] Re: strange result from PSCBS
Hi, it's not easy to say. My point is that you look at the normal data, i.e. BAF (but also TCN relative to a global reference), you may have more clues on the quality of the normal sample. If that is bad, then then tumor-normal TCN is most likely bad too. /Henrik On Tue, Feb 24, 2015 at 7:42 AM, Chengyu Liu wrote: > I understand DH is defined only for heterozygous SNPs. But the total copy > number estimates look ok. Do you think I need to discard this sample or not > when I do total copy number analysis? I will discard this sample when I do > parent-specific analysis. But not sure whether I should leave this sample > out for alteration calls. > > You are expert of PSCBS, can you give me suggestion here? > > Br, > C.Y > > On Monday, February 23, 2015 at 9:54:47 PM UTC+2, Henrik Bengtsson wrote: >> >> Hi, >> >> DH signals are only defined for heterozygous SNPs, so lack of DHs >> indicates a problem with the matched normal BAFs (see my other email). >> >> /Henrik >> >> On Mon, Feb 23, 2015 at 1:53 AM, Chengyu Liu wrote: >> > It is difficult for me to say whether it is failed or the normal sample >> > is >> > nose. Can you have a look at these four figures ? They are from two >> > paired >> > tumor samples. One of them is missing DH . In the other sample, minor cn >> > is >> > 0 and major cn is 1. I am also attaching the total copy number estimate. >> > >> > Br, >> > Chengyu >> > >> > On Wednesday, February 18, 2015 at 11:25:48 PM UTC+2, Henrik Bengtsson >> > wrote: >> >> >> >> DH is only defined from heterozygous SNPs. If you don't see any DH >> >> signals, that indicates that none of the SNPs where called >> >> heterozygous. This could be an indicatation of a failed or a very >> >> noise normal sample. >> >> >> >> /Henrik >> > >> > -- >> > -- >> > When reporting problems on aroma.affymetrix, make sure 1) to run the >> > latest >> > version of the package, 2) to report the output of sessionInfo() and >> > traceback(), and 3) to post a complete code example. >> > >> > >> > You received this message because you are subscribed to the Google >> > Groups >> > "aroma.affymetrix" group with website http://www.aroma-project.org/. >> > To post to this group, send email to aroma-af...@googlegroups.com >> > To unsubscribe and other options, go to >> > http://www.aroma-project.org/forum/ >> > >> > --- >> > You received this message because you are subscribed to the Google >> > Groups >> > "aroma.affymetrix" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to aroma-affymetr...@googlegroups.com. >> > For more options, visit https://groups.google.com/d/optout. > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] Re: strange result from PSCBS
Hi, DH signals are only defined for heterozygous SNPs, so lack of DHs indicates a problem with the matched normal BAFs (see my other email). /Henrik On Mon, Feb 23, 2015 at 1:53 AM, Chengyu Liu wrote: > It is difficult for me to say whether it is failed or the normal sample is > nose. Can you have a look at these four figures ? They are from two paired > tumor samples. One of them is missing DH . In the other sample, minor cn is > 0 and major cn is 1. I am also attaching the total copy number estimate. > > Br, > Chengyu > > On Wednesday, February 18, 2015 at 11:25:48 PM UTC+2, Henrik Bengtsson > wrote: >> >> DH is only defined from heterozygous SNPs. If you don't see any DH >> signals, that indicates that none of the SNPs where called >> heterozygous. This could be an indicatation of a failed or a very >> noise normal sample. >> >> /Henrik > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] Re: strange result from PSCBS
DH is only defined from heterozygous SNPs. If you don't see any DH signals, that indicates that none of the SNPs where called heterozygous. This could be an indicatation of a failed or a very noise normal sample. /Henrik -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] Errors occurred in the PSCBS analysis
I'll try to catch up with a few questions; comments below.
On Mon, Feb 9, 2015 at 3:52 AM, Chengyu Liu wrote:
> Hi,
>
> I am doing allele-specific analysis using PSCBS package. I have paired
> tumor-normal matched samples.
> For one of the samples, i got an error which is like
>
> at #06. lapply(names.T[8:length(names.T)], function(x) {
> print(x)
> y <- grep(x, names(df))
> if (length(y) != 3) {
> stop("Length of y is not 3")
> }
> d <- dropSegmentationOutliers(y = df[, y[1]], chromosome =
> df[,
> 1], x = df[, 2])
> d <- data.frame(chromosome = df[, 1], x = df[, 2], CT = d,
> betaT = df[, y[2]], betaN = df[, y[3]])
> fit <- segmentByPairedPSCBS(CT = d[, 3], betaT = d[, 4],
> betaN = d[, 5], chromosome = d$chromosome, x = d$x)
> segs <- getSegments(fit)
> pairName <- x
> chrTag <- sprintf("Chr%s",
> seqToHumanReadable(getChromosomes(fit)))
> toPNG(pairName, tags = c(chrTag, "PairedPSCBS"), width = 840,
> aspectRatio = 0.6, {
> plotTracks(fit)
> })
> ret <- data.frame(sample = x, segs)
> return(ret)
> })
> - lapply() is in environment 'base'
> - originating from 'cytoscanHD.processing.R'
>
> at #05. aroma.affy.snp.preprocessing(path =
> "/storageBig/storageBig1/czliu/input/azhar/aroma/",
> chipType = "CytoScanHD_Array", dataSet = "dataset1",
> combineAlleles = FALSE,
> paired = TRUE, verbose = FALSE, PSCNA = FALSE, na.rm = TRUE)
> - aroma.affy.snp.preprocessing() is in environment 'R_GlobalEnv'
> - originating from 'cytoscanHD.processing.R'
>
> at #04. eval(expr, envir, enclos)
> - eval() is local of the calling function
>
> at #03. eval(ei, envir)
> - eval() is in environment 'base'
>
> at #02. withVisible(eval(ei, envir))
> - withVisible() is in environment 'base'
>
> at #01. source("cytoscanHD.processing.R")
> - source() is in environment 'base'
>
> Error: All genotypes ('muN') called from the normal allele B fractions
> ('betaN') are NAs: 2819494 (100%) out of 2819494
> In addition: There were 30 warnings (use warnings() to see them)
>
> It seems all BAF values were NA. Why does it happen ? Is there something
> wrong with the sample ?
This is a sanity check kicking in preventing a likely error in
data/annotation from propagating further in your analysis. As genome
types are called from the normal BAFs, i.e. betaN = d[, 5] in your
case. Have a look at those BAF signals, e.g. plotDensity(betaN) to
see if they're showing the three expected BAF modes near 0%, 50% and
100%. If your data is extremely noisy genotype calling will fail.
Internally, segmentByPairedPSCBS() uses:
muN <- aroma.light::callNaiveGenotypes(betaN, censorAt=c(0,1))
so you can look at the calls made that way too.
Hope this helps
/Henrik
>
>
> Br,
> Chengyu
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> ---
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to aroma-affymetrix+unsubscr...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
---
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Re: [aroma.affymetrix] After running doCRMAv2, I got chromosome 24,25
Chr 23 = Chr X Chr 24 = Chr Y Chr 25 = Chr M (Mitochondrial) /Henrik On Wed, Feb 4, 2015 at 12:27 AM, Chengyu Liu wrote: > Hi, > > After I ran doCRMAv2, and exported the raw copy number. Everything is ok but > there are chromosome 24 and 25. I suppose 23 is chromosome X.I do not > understand why are 24 and 25 chromosomes from? > I am using CytoScan HD array > > Br, > Chengyu > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] fit CBS model error
Good to hear.
I'll fix/workaround this peculiar problem so this won't the future.
It might be a while before you see the fix, but it's added to my todo
list [https://github.com/HenrikBengtsson/R.oo/issues/5].
/Henrik
On Mon, Jan 26, 2015 at 9:00 AM, Jerry Liu wrote:
> It worked! I did load the annotation package and hgu133a for other analysis.
> Couldt be some name space collision. Restarting seems to work. Now it had
> passed that error and running...
>
> Thanks again very much!
> Jerry
>
> On Monday, January 26, 2015 at 11:32:25 AM UTC-5, Henrik Bengtsson wrote:
>>
>> On Mon, Jan 26, 2015 at 7:56 AM, Jerry Liu wrote:
>> > Hi Henrik ,
>> >
>> > Thanks very much for your such quick reply! It could be a Bioconductor
>> > error. I'd appreciate it greatly if you could give me some suggestions
>> > on
>> > how to fix this.
>>
>> I think I understand the problem(*). The immediate
>> solution/workaround for you is to retry in a fresh R session such that
>> there are no package already loaded, particularly not all those
>> Bioconductor annotation data packages. That should do it.
>>
>> Henrik
>>
>> (*) The solution is to make the R.oo package (mine) to also handle
>> deprecated setups in Bioconductor - aready too much technical details.
>>
>> >
>> > Here's the trace back:
>> >
>> > 19: stop(paste(msg, collapse = ""), call. = FALSE, domain = NA)
>> > 18: .Defunct(msg = msg)
>> > 17: (function ()
>> > {
>> > if (grepl("PFAM", x)) {
>> > bimapName <- paste0(prefix, "PFAM")
>> > }
>> > else {
>> > bimapName <- paste0(prefix, "PROSITE")
>> > }
>> > x <- dc[[bimapName]]
>> > msg = wmsg(paste0(bimapName, " is defunct. ", "Please use
>> > select()
>> > if you need access to PFAM or PROSITE accessions. \n"))
>> > if (interactive()) {
>> > .Defunct(msg = msg)
>> > }
>> > })()
>> > 16: eval(expr, envir, enclos)
>> > 15: eval(expr, envir = envir)
>> > 14: FUN(c("hgu133a", "hgu133aACCNUM", "hgu133aALIAS2PROBE",
>> > "hgu133aCHR",
>> > "hgu133aCHRLENGTHS", "hgu133aCHRLOC", "hgu133aCHRLOCEND",
>> > "hgu133a.db",
>> > "hgu133a_dbconn", "hgu133a_dbfile", "hgu133a_dbInfo",
>> > "hgu133a_dbschema",
>> > "hgu133aENSEMBL", "hgu133aENSEMBL2PROBE", "hgu133aENTREZID",
>> > "hgu133aENZYME", "hgu133aENZYME2PROBE", "hgu133aGENENAME",
>> > "hgu133aGO",
>> > "hgu133aGO2ALLPROBES", "hgu133aGO2PROBE", "hgu133aMAP",
>> > "hgu133aMAPCOUNTS",
>> > "hgu133aOMIM", "hgu133aORGANISM", "hgu133aORGPKG", "hgu133aPATH",
>> > "hgu133aPATH2PROBE", "hgu133aPFAM", "hgu133aPMID",
>> > "hgu133aPMID2PROBE",
>> > "hgu133aPROSITE", "hgu133aREFSEQ", "hgu133aSYMBOL",
>> > "hgu133aUNIGENE",
>> > "hgu133aUNIPROT")[[29L]], ...)
>> > 13: lapply(X = X, FUN = FUN, ...)
>> > 12: sapply(objectNames, FUN = function(objectName) {
>> > expr <- substitute({
>> > is.function(x) && inherits(x, "Class")
>> > }, list(x = as.name(objectName)))
>> > eval(expr, envir = envir)
>> > })
>> > 11: getKnownSubclassesInEnvironment(name, envir = envir)
>> > 10: getKnownSubclasses.Class(clazz)
>> > 9: getKnownSubclasses(clazz)
>> > 8: getFileListClass.GenericDataFileSetList(this)
>> > 7: getFileListClass(this)
>> > 6: getFileList.GenericDataFileSetList(cesTuple, array, ..., verbose =
>> > less(verbose,
>> >1))
>> > 5: getFileList(cesTuple, array, ..., verbose = less(verbose, 1))
>> > 4: getDataFileMatrix.CopyNumberChromosomalModel(this, array = array,
>> >verbose = less(verbose, 5))
>> > 3: getDataFileMatrix(this, array = array, verbose = less(verbose,
>> >5))
>> > 2: fit.CopyNumberSegmentationModel(sm, verbose = -10)
>> > 1: fit(sm, verbose = -10)
>> >
>> >
>> > On Mon, Jan 26,
Re: [aroma.affymetrix] fit CBS model error
packages:
>> [1] DNAcopy_1.40.0 preprocessCore_1.28.0
>> [3] sfit_0.3.0 aroma.light_2.2.0
>> [5] aroma.affymetrix_2.12.0 aroma.core_2.12.1
>> [7] R.devices_2.12.0R.filesets_2.6.0
>> [9] R.utils_1.34.0 R.oo_1.18.0
>> [11] affxparser_1.38.0 R.methodsS3_1.6.1
>> [13] hgu133a.db_3.0.0org.Hs.eg.db_3.0.0
>> [15] RSQLite_1.0.0 DBI_0.3.1
>> [17] gage_2.16.0 annotate_1.44.0
>> [19] XML_3.98-1.1AnnotationDbi_1.28.1
>> [21] GenomeInfoDb_1.2.3 IRanges_2.0.0
>> [23] S4Vectors_0.4.0 hgu133acdf_2.15.0
>> [25] affy_1.44.0 Biobase_2.26.0
>> [27] BiocGenerics_0.12.1
>>
>> loaded via a namespace (and not attached):
>> [1] affyio_1.34.0aroma.apd_0.5.0
>> [3] base64enc_0.1-2 BiocInstaller_1.16.1
>> [5] Biostrings_2.34.0Cairo_1.5-6
>> [7] digest_0.6.4 graph_1.44.0
>> [9] httr_0.5 KEGGREST_1.6.1
>> [11] matrixStats_0.12.2 png_0.1-7
>> [13] PSCBS_0.43.0 R.cache_0.10.0
>> [15] R.huge_0.8.0 R.rsp_0.19.0
>> [17] splines_3.1.1stringr_0.6.2
>> [19] tools_3.1.1 xtable_1.7-4
>> [21] XVector_0.6.0zlibbioc_1.12.0
>>
>> --
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to aroma-affymetrix@googlegroups.com
>> To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>>
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to aroma-affymetrix+unsubscr...@googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>
>
>
> On Monday, January 26, 2015 at 10:46:46 AM UTC-5, Henrik Bengtsson wrote:
>>
>> On Mon, Jan 26, 2015 at 7:31 AM, Jerry Liu wrote:
>> >
>> > Hello,
>> >
>> > I got an error after trying to fit the CBS model:
>> >
>> > Error: hgu133aPFAM is defunct. Please use select() if you
>> > need access to PFAM or PROSITE accessions.
>> >
>> > Here are the command I ran:
>> >
>> > ds<-doCRMAv2("GSE57277_DLBCL", chipType="Mapping250K_Sty",
>> > plm="RmaCnPlm")
>> > sm<-CbsModel(ds)
>> > fit(sm, verbose=-10)
>> >
>> > I have no clue of how to use select() as per the error message to fix
>> > this problem. My R session info is at the bottom of the email. Please help,
>> > many thanks!
>>
>> This does not an error message for the Aroma Framework, but more
>> likely something from a Bioconductor package. It's not obvious to me
>> how that is triggered by the above call. Could you please send what
>> traceback() outputs immediately after you get the error.
>>
>> /Henrik
>>
>> >
>> > Jerry
>> >
>> >
>> > sessionInfo():
>> > R version 3.1.1 (2014-07-10)
>> > Platform: x86_64-unknown-linux-gnu (64-bit)
>> >
>> > locale:
>> > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> > [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>> > [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>> > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> > [9] LC_ADDRESS=C LC_TELEPHONE=C
>> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>> >
>> > attached base packages:
>> > [1] stats4parallel stats graphics grDevices
>> > [6] utils datasets methods base
>> >
>> > other attached packages:
>> > [1] DNAcopy_1.40.0 preprocessCore_1.28.0
>> > [3] sfit_0.3.0 aroma.light_2.2.0
>> > [5] aroma.affymetrix_2.12.0 aroma.core_2.12.1
>> > [7] R.devices_2.12.0R.filesets_2.6.0
>> > [9] R.utils_1.34.0 R.oo_1.18.0
>> > [11] affxparser_1.38.0 R.methodsS3_1.6.1
>> > [13] hgu133a.db_3.0.0org.Hs.eg.db_3.0.0
>> > [15] RSQLite_1.0.0 DBI_0.3.1
>> > [17] gage_2.16.0 annotate_1.44.0
>> > [19] XML_3.98
Re: [aroma.affymetrix] fit CBS model error
On Mon, Jan 26, 2015 at 7:31 AM, Jerry Liu wrote:
>
> Hello,
>
> I got an error after trying to fit the CBS model:
>
> Error: hgu133aPFAM is defunct. Please use select() if you
> need access to PFAM or PROSITE accessions.
>
> Here are the command I ran:
>
> ds<-doCRMAv2("GSE57277_DLBCL", chipType="Mapping250K_Sty", plm="RmaCnPlm")
> sm<-CbsModel(ds)
> fit(sm, verbose=-10)
>
> I have no clue of how to use select() as per the error message to fix this
> problem. My R session info is at the bottom of the email. Please help, many
> thanks!
This does not an error message for the Aroma Framework, but more
likely something from a Bioconductor package. It's not obvious to me
how that is triggered by the above call. Could you please send what
traceback() outputs immediately after you get the error.
/Henrik
>
> Jerry
>
>
> sessionInfo():
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats4parallel stats graphics grDevices
> [6] utils datasets methods base
>
> other attached packages:
> [1] DNAcopy_1.40.0 preprocessCore_1.28.0
> [3] sfit_0.3.0 aroma.light_2.2.0
> [5] aroma.affymetrix_2.12.0 aroma.core_2.12.1
> [7] R.devices_2.12.0R.filesets_2.6.0
> [9] R.utils_1.34.0 R.oo_1.18.0
> [11] affxparser_1.38.0 R.methodsS3_1.6.1
> [13] hgu133a.db_3.0.0org.Hs.eg.db_3.0.0
> [15] RSQLite_1.0.0 DBI_0.3.1
> [17] gage_2.16.0 annotate_1.44.0
> [19] XML_3.98-1.1AnnotationDbi_1.28.1
> [21] GenomeInfoDb_1.2.3 IRanges_2.0.0
> [23] S4Vectors_0.4.0 hgu133acdf_2.15.0
> [25] affy_1.44.0 Biobase_2.26.0
> [27] BiocGenerics_0.12.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.34.0aroma.apd_0.5.0
> [3] base64enc_0.1-2 BiocInstaller_1.16.1
> [5] Biostrings_2.34.0Cairo_1.5-6
> [7] digest_0.6.4 graph_1.44.0
> [9] httr_0.5 KEGGREST_1.6.1
> [11] matrixStats_0.12.2 png_0.1-7
> [13] PSCBS_0.43.0 R.cache_0.10.0
> [15] R.huge_0.8.0 R.rsp_0.19.0
> [17] splines_3.1.1stringr_0.6.2
> [19] tools_3.1.1 xtable_1.7-4
> [21] XVector_0.6.0zlibbioc_1.12.0
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
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>
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--
--
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Re: [aroma.affymetrix] Questions on extracting probeset summaries
Great. I've now made aroma.affymetrix 2.13.1 available, which is
installed the usual way:
source('http://callr.org/install#aroma.affymetrix";)
Anyone who reads this should update this way.
/Henrik
On Fri, Jan 23, 2015 at 2:57 PM, Qingzhou Zhang wrote:
> Thanks!
>
> Seems working pretty well.
>
>> cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2")
>> cdfM <- getMonocellCdf(cdf, verbose=TRUE)
> Retrieving monocell CDF...
> Monocell chip type: HG-U133_Plus_2,monocell
> Locating monocell CDF...
> Pathname:
> Locating monocell CDF...done
> Could not locate monocell CDF. Will create one for chip type...
> Could not locate monocell CDF. Will create one for chip type...done
> Retrieving monocell CDF...done
>> print(cdfM)
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/HG-U133_Plus_2
> Filename: HG-U133_Plus_2,monocell.CDF
> File size: 9.63 MB (10098009 bytes)
> Chip type: HG-U133_Plus_2,monocell
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 246x245
> Number of cells: 60270
> Number of units: 54675
> Cells per unit: 1.10
> Number of QC units: 9
>
>
>
> On Saturday, 24 January 2015 03:52:43 UTC+8, Henrik Bengtsson wrote:
>>
>> Solved. Before finalize a release, would you mind making sure it
>> works on your end. Install aroma.affymetrix 2.13.0-9001 by running
>> the following in a fresh R session:
>>
>>
>> source('http://callr.org/install#HenrikBengtsson/aroma.affymetrix@2.13.0-9001')
>>
>> Then retry with
>>
>> library("aroma.affymetrix")
>> cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2")
>> cdfM <- getMonocellCdf(cdf, verbose=TRUE)
>> print(cdfM)
>>
>> If it complains about a pre-existing *.tmp file, remove that one an retry.
>>
>> As soon as you confirm it works, I'll make aroma.affymetrix 2.13.1
>> available, because this was a critical bug(*).
>>
>> Thanks for the report
>>
>> /Henrik
>>
>> (*) DETAILS: Turns out to be due to a single stray newline. It should have
>> been
>>
>> affxparser::writeCdfUnits(...)
>>
>> but it was:
>>
>> affxparser::writeCdfUnits
>> (...)
>>
>> Despite running 24 hours of regular package testing, this piece of
>> code was never tested. I've now added an explicit test on creating
>> and re-creating monocell CDF.
>>
>> On Fri, Jan 23, 2015 at 8:49 AM, Henrik Bengtsson
>> wrote:
>> > I managed to reproduce this now:
>> >
>> > Error in (...) : 3 arguments passed to '(' which requires 1
>> > 20150123 08:48:49| Could not locate monocell CDF. Will create one for
>> > chip type.
>> > ..done
>> > 20150123 08:48:49|Retrieving monocell CDF...done
>> >> traceback()
>> > 5: .writeCdfUnits(con = con, srcUnits, verbose = verbose2)
>> > 4: createMonocellCdf.AffymetrixCdfFile(this, ..., verbose =
>> > less(verbose))
>> > 3: createMonocellCdf(this, ..., verbose = less(verbose))
>> > 2: getMonocellCdf.AffymetrixCdfFile(cdf, verbose =
>> > Arguments$getVerbose(-8,
>> >timestamp = TRUE))
>> > 1: getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8, timestamp =
>> > TRUE))
>> >
>> > I'll investigate and fix this asap.
>> >
>> > /Henrik
>> >
>> >
>> > On Fri, Jan 23, 2015 at 7:37 AM, Henrik Bengtsson
>> > wrote:
>> >>
>> >> On Jan 23, 2015 7:36 AM, "Henrik Bengtsson"
>> >> wrote:
>> >>>
>> >>> This is odd for several reasons, e.g. I'm puzzled how you ended up
>> >>> with a
>> >>> monocell CDF previously but now it gives an error. Let's troubleshoot
>> >>> more...
>> >>>
>> >>> What does troubleshoot() output directly after you get that error?
>> >>
>> >> I meant traceback()
>> >>
>> >>>
>> >>> Henrik
>> >>>
>> >>> On Jan 23, 2015 7:23 AM, "Qingzhou Zhang" wrote:
>> >>> >
>> >>> > Thanks, Henrik,
>> >>> >
>> >>> > It seems that something went wrong with the monocell cdf file by
>> >>> > troubleshooting:
>> >>> >
>> >>> >
>> >>> > > cdf
>> >>> >
>> >>> > AffymetrixCdfFile:
>> >>> >
>> >>> > Path: annotationData/chi
Re: [aroma.affymetrix] Questions on extracting probeset summaries
Solved. Before finalize a release, would you mind making sure it
works on your end. Install aroma.affymetrix 2.13.0-9001 by running
the following in a fresh R session:
source('http://callr.org/install#HenrikBengtsson/aroma.affymetrix@2.13.0-9001')
Then retry with
library("aroma.affymetrix")
cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2")
cdfM <- getMonocellCdf(cdf, verbose=TRUE)
print(cdfM)
If it complains about a pre-existing *.tmp file, remove that one an retry.
As soon as you confirm it works, I'll make aroma.affymetrix 2.13.1
available, because this was a critical bug(*).
Thanks for the report
/Henrik
(*) DETAILS: Turns out to be due to a single stray newline. It should have been
affxparser::writeCdfUnits(...)
but it was:
affxparser::writeCdfUnits
(...)
Despite running 24 hours of regular package testing, this piece of
code was never tested. I've now added an explicit test on creating
and re-creating monocell CDF.
On Fri, Jan 23, 2015 at 8:49 AM, Henrik Bengtsson wrote:
> I managed to reproduce this now:
>
> Error in (...) : 3 arguments passed to '(' which requires 1
> 20150123 08:48:49| Could not locate monocell CDF. Will create one for chip
> type.
> ..done
> 20150123 08:48:49|Retrieving monocell CDF...done
>> traceback()
> 5: .writeCdfUnits(con = con, srcUnits, verbose = verbose2)
> 4: createMonocellCdf.AffymetrixCdfFile(this, ..., verbose = less(verbose))
> 3: createMonocellCdf(this, ..., verbose = less(verbose))
> 2: getMonocellCdf.AffymetrixCdfFile(cdf, verbose = Arguments$getVerbose(-8,
>timestamp = TRUE))
> 1: getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8, timestamp = TRUE))
>
> I'll investigate and fix this asap.
>
> /Henrik
>
>
> On Fri, Jan 23, 2015 at 7:37 AM, Henrik Bengtsson
> wrote:
>>
>> On Jan 23, 2015 7:36 AM, "Henrik Bengtsson" wrote:
>>>
>>> This is odd for several reasons, e.g. I'm puzzled how you ended up with a
>>> monocell CDF previously but now it gives an error. Let's troubleshoot
>>> more...
>>>
>>> What does troubleshoot() output directly after you get that error?
>>
>> I meant traceback()
>>
>>>
>>> Henrik
>>>
>>> On Jan 23, 2015 7:23 AM, "Qingzhou Zhang" wrote:
>>> >
>>> > Thanks, Henrik,
>>> >
>>> > It seems that something went wrong with the monocell cdf file by
>>> > troubleshooting:
>>> >
>>> >
>>> > > cdf
>>> >
>>> > AffymetrixCdfFile:
>>> >
>>> > Path: annotationData/chipTypes/HG-U133_Plus_2
>>> >
>>> > Filename: HG-U133_Plus_2,monocell.CDF
>>> >
>>> > File size: 4.88 MB (5116945 bytes)
>>> >
>>> > Chip type: HG-U133_Plus_2,monocell
>>> >
>>> > RAM: 0.46MB
>>> >
>>> > File format: v4 (binary; XDA)
>>> >
>>> > Dimension: 182x182
>>> >
>>> > Number of cells: 33124
>>> >
>>> > Number of units: 27604
>>> >
>>> > Cells per unit: 1.20
>>> >
>>> > Number of QC units: 9
>>> >
>>> >
>>> >
>>> > So I have deleted the previous monocell cdf file in
>>> > annotationData/chipTypes/HG-U133_Plus_2 and re-create it by the following:
>>> >
>>> > cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2")
>>> >
>>> > cdfM <- getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8, timestamp
>>> > = TRUE))
>>> >
>>> >
>>> >
>>> > However, the above process also failed, here is the output:
>>> >
>>> > > cdfM <- getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8,
>>> > > timestamp = TRUE))
>>> >
>>> > 20150123 21:47:53|Retrieving monocell CDF...
>>> >
>>> > 20150123 21:47:53| Monocell chip type: HG-U133_Plus_2,monocell
>>> >
>>> > 20150123 21:47:53| Locating monocell CDF...
>>> >
>>> > 20150123 21:47:53| Pathname:
>>> >
>>> > 20150123 21:47:53| Locating monocell CDF...done
>>> >
>>> > 20150123 21:47:53| Could not locate monocell CDF. Will create one for
>>> > chip type...
>>> >
>>> > 20150123 21:47:53| Creating monocell CDF...
>>> >
>>> > 20150123 21:47:53| Chip type: HG-U133_Plus_2
>>> >
>>> > 20150123 21:47:53| Validate (m
Re: [aroma.affymetrix] Questions on extracting probeset summaries
I managed to reproduce this now:
Error in (...) : 3 arguments passed to '(' which requires 1
20150123 08:48:49| Could not locate monocell CDF. Will create one for chip type.
..done
20150123 08:48:49|Retrieving monocell CDF...done
> traceback()
5: .writeCdfUnits(con = con, srcUnits, verbose = verbose2)
4: createMonocellCdf.AffymetrixCdfFile(this, ..., verbose = less(verbose))
3: createMonocellCdf(this, ..., verbose = less(verbose))
2: getMonocellCdf.AffymetrixCdfFile(cdf, verbose = Arguments$getVerbose(-8,
timestamp = TRUE))
1: getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8, timestamp = TRUE))
I'll investigate and fix this asap.
/Henrik
On Fri, Jan 23, 2015 at 7:37 AM, Henrik Bengtsson wrote:
>
> On Jan 23, 2015 7:36 AM, "Henrik Bengtsson" wrote:
>>
>> This is odd for several reasons, e.g. I'm puzzled how you ended up with a
>> monocell CDF previously but now it gives an error. Let's troubleshoot
>> more...
>>
>> What does troubleshoot() output directly after you get that error?
>
> I meant traceback()
>
>>
>> Henrik
>>
>> On Jan 23, 2015 7:23 AM, "Qingzhou Zhang" wrote:
>> >
>> > Thanks, Henrik,
>> >
>> > It seems that something went wrong with the monocell cdf file by
>> > troubleshooting:
>> >
>> >
>> > > cdf
>> >
>> > AffymetrixCdfFile:
>> >
>> > Path: annotationData/chipTypes/HG-U133_Plus_2
>> >
>> > Filename: HG-U133_Plus_2,monocell.CDF
>> >
>> > File size: 4.88 MB (5116945 bytes)
>> >
>> > Chip type: HG-U133_Plus_2,monocell
>> >
>> > RAM: 0.46MB
>> >
>> > File format: v4 (binary; XDA)
>> >
>> > Dimension: 182x182
>> >
>> > Number of cells: 33124
>> >
>> > Number of units: 27604
>> >
>> > Cells per unit: 1.20
>> >
>> > Number of QC units: 9
>> >
>> >
>> >
>> > So I have deleted the previous monocell cdf file in
>> > annotationData/chipTypes/HG-U133_Plus_2 and re-create it by the following:
>> >
>> > cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2")
>> >
>> > cdfM <- getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8, timestamp
>> > = TRUE))
>> >
>> >
>> >
>> > However, the above process also failed, here is the output:
>> >
>> > > cdfM <- getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8,
>> > > timestamp = TRUE))
>> >
>> > 20150123 21:47:53|Retrieving monocell CDF...
>> >
>> > 20150123 21:47:53| Monocell chip type: HG-U133_Plus_2,monocell
>> >
>> > 20150123 21:47:53| Locating monocell CDF...
>> >
>> > 20150123 21:47:53| Pathname:
>> >
>> > 20150123 21:47:53| Locating monocell CDF...done
>> >
>> > 20150123 21:47:53| Could not locate monocell CDF. Will create one for
>> > chip type...
>> >
>> > 20150123 21:47:53| Creating monocell CDF...
>> >
>> > 20150123 21:47:53| Chip type: HG-U133_Plus_2
>> >
>> > 20150123 21:47:53| Validate (main) CDF...
>> >
>> > 20150123 21:47:54| Validate (main) CDF...done
>> >
>> > 20150123 21:47:55| Adding temporary suffix from file...
>> >
>> > 20150123 21:47:55|Pathname:
>> > annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2,monocell.CDF
>> >
>> > 20150123 21:47:55|Suffix: .tmp
>> >
>> > 20150123 21:47:55|Rename existing file?: FALSE
>> >
>> > 20150123 21:47:55|Temporary pathname:
>> > annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2,monocell.CDF.tmp
>> >
>> > 20150123 21:47:55| Adding temporary suffix from file...done
>> >
>> > 20150123 21:47:55| Number of cells per group field: 1
>> >
>> > 20150123 21:47:55| Reading CDF group names...
>> >
>> > 20150123 21:47:55| Reading CDF group names...done
>> >
>> > used (Mb) gc trigger (Mb) max used (Mb)
>> >
>> >Ncells 603933 32.3 899071 48.1 741108 39.6
>> >
>> >Vcells 1027587 7.91757946 13.5 1424724 10.9
>> >
>> > used (Mb) gc trigger (Mb) max used (Mb)
>> >
>> >Ncells 549349 29.4 899071 48.1 899071 48.1
>> >
>> >Vcells 945722 7.31757946 13.5 1424724 10.9
>> >
>> > 20150123 21:47:56| Number of cells per unit:
>>
Re: [aroma.affymetrix] Questions on extracting probeset summaries
On Jan 23, 2015 7:36 AM, "Henrik Bengtsson" wrote:
>
> This is odd for several reasons, e.g. I'm puzzled how you ended up with a
monocell CDF previously but now it gives an error. Let's troubleshoot
more...
>
> What does troubleshoot() output directly after you get that error?
I meant traceback()
>
> Henrik
>
> On Jan 23, 2015 7:23 AM, "Qingzhou Zhang" wrote:
> >
> > Thanks, Henrik,
> >
> > It seems that something went wrong with the monocell cdf file by
troubleshooting:
> >
> >
> > > cdf
> >
> > AffymetrixCdfFile:
> >
> > Path: annotationData/chipTypes/HG-U133_Plus_2
> >
> > Filename: HG-U133_Plus_2,monocell.CDF
> >
> > File size: 4.88 MB (5116945 bytes)
> >
> > Chip type: HG-U133_Plus_2,monocell
> >
> > RAM: 0.46MB
> >
> > File format: v4 (binary; XDA)
> >
> > Dimension: 182x182
> >
> > Number of cells: 33124
> >
> > Number of units: 27604
> >
> > Cells per unit: 1.20
> >
> > Number of QC units: 9
> >
> >
> >
> > So I have deleted the previous monocell cdf file in
annotationData/chipTypes/HG-U133_Plus_2 and re-create it by the following:
> >
> > cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2")
> >
> > cdfM <- getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8,
timestamp = TRUE))
> >
> >
> >
> > However, the above process also failed, here is the output:
> >
> > > cdfM <- getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8,
timestamp = TRUE))
> >
> > 20150123 21:47:53|Retrieving monocell CDF...
> >
> > 20150123 21:47:53| Monocell chip type: HG-U133_Plus_2,monocell
> >
> > 20150123 21:47:53| Locating monocell CDF...
> >
> > 20150123 21:47:53| Pathname:
> >
> > 20150123 21:47:53| Locating monocell CDF...done
> >
> > 20150123 21:47:53| Could not locate monocell CDF. Will create one for
chip type...
> >
> > 20150123 21:47:53| Creating monocell CDF...
> >
> > 20150123 21:47:53| Chip type: HG-U133_Plus_2
> >
> > 20150123 21:47:53| Validate (main) CDF...
> >
> > 20150123 21:47:54| Validate (main) CDF...done
> >
> > 20150123 21:47:55| Adding temporary suffix from file...
> >
> > 20150123 21:47:55|Pathname:
annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2,monocell.CDF
> >
> > 20150123 21:47:55|Suffix: .tmp
> >
> > 20150123 21:47:55|Rename existing file?: FALSE
> >
> > 20150123 21:47:55|Temporary pathname:
annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2,monocell.CDF.tmp
> >
> > 20150123 21:47:55| Adding temporary suffix from file...done
> >
> > 20150123 21:47:55| Number of cells per group field: 1
> >
> > 20150123 21:47:55| Reading CDF group names...
> >
> > 20150123 21:47:55| Reading CDF group names...done
> >
> > used (Mb) gc trigger (Mb) max used (Mb)
> >
> >Ncells 603933 32.3 899071 48.1 741108 39.6
> >
> >Vcells 1027587 7.91757946 13.5 1424724 10.9
> >
> > used (Mb) gc trigger (Mb) max used (Mb)
> >
> >Ncells 549349 29.4 899071 48.1 899071 48.1
> >
> >Vcells 945722 7.31757946 13.5 1424724 10.9
> >
> > 20150123 21:47:56| Number of cells per unit:
> >
> > Min. 1st Qu. MedianMean 3rd Qu.Max.
> >
> > 1 1 1 1 1 1
> >
> > 20150123 21:47:56| Reading CDF QC units...
> >
> > 20150123 21:47:56| Reading CDF QC units...done
> >
> > 20150123 21:47:56| Number of QC cells: 5385 in 9 QC units (0.1MB)
> >
> > 20150123 21:47:56| Total number of cells: 60060
> >
> > 20150123 21:47:56| Best array dimension: 246x245 (=60270 cells, i.e.
210 left-over cells)
> >
> > 20150123 21:47:56| Creating CDF header with source CDF as template...
> >
> > 20150123 21:47:56|Setting up header...
> >
> > 20150123 21:47:56| Reading CDF header...
> >
> > 20150123 21:47:56| Reading CDF header...done
> >
> > 20150123 21:47:56| Reading CDF unit names...
> >
> > 20150123 21:47:56| Reading CDF unit names...done
> >
> > 20150123 21:47:56|Setting up header...done
> >
> > 20150123 21:47:56|Writing...
> >
> > 20150123 21:47:56| destHeader:
> >
> > List of 12
> >
> > $ ncols : int 245
> >
> > $ nrows : int 246
> >
> >
Re: [aroma.affymetrix] Questions on extracting probeset summaries
This is odd for several reasons, e.g. I'm puzzled how you ended up with a
monocell CDF previously but now it gives an error. Let's troubleshoot
more...
What does troubleshoot() output directly after you get that error?
Henrik
On Jan 23, 2015 7:23 AM, "Qingzhou Zhang" wrote:
>
> Thanks, Henrik,
>
> It seems that something went wrong with the monocell cdf file by
troubleshooting:
>
>
> > cdf
>
> AffymetrixCdfFile:
>
> Path: annotationData/chipTypes/HG-U133_Plus_2
>
> Filename: HG-U133_Plus_2,monocell.CDF
>
> File size: 4.88 MB (5116945 bytes)
>
> Chip type: HG-U133_Plus_2,monocell
>
> RAM: 0.46MB
>
> File format: v4 (binary; XDA)
>
> Dimension: 182x182
>
> Number of cells: 33124
>
> Number of units: 27604
>
> Cells per unit: 1.20
>
> Number of QC units: 9
>
>
>
> So I have deleted the previous monocell cdf file in
annotationData/chipTypes/HG-U133_Plus_2 and re-create it by the following:
>
> cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2")
>
> cdfM <- getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8, timestamp
= TRUE))
>
>
>
> However, the above process also failed, here is the output:
>
> > cdfM <- getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8,
timestamp = TRUE))
>
> 20150123 21:47:53|Retrieving monocell CDF...
>
> 20150123 21:47:53| Monocell chip type: HG-U133_Plus_2,monocell
>
> 20150123 21:47:53| Locating monocell CDF...
>
> 20150123 21:47:53| Pathname:
>
> 20150123 21:47:53| Locating monocell CDF...done
>
> 20150123 21:47:53| Could not locate monocell CDF. Will create one for
chip type...
>
> 20150123 21:47:53| Creating monocell CDF...
>
> 20150123 21:47:53| Chip type: HG-U133_Plus_2
>
> 20150123 21:47:53| Validate (main) CDF...
>
> 20150123 21:47:54| Validate (main) CDF...done
>
> 20150123 21:47:55| Adding temporary suffix from file...
>
> 20150123 21:47:55|Pathname:
annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2,monocell.CDF
>
> 20150123 21:47:55|Suffix: .tmp
>
> 20150123 21:47:55|Rename existing file?: FALSE
>
> 20150123 21:47:55|Temporary pathname:
annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2,monocell.CDF.tmp
>
> 20150123 21:47:55| Adding temporary suffix from file...done
>
> 20150123 21:47:55| Number of cells per group field: 1
>
> 20150123 21:47:55| Reading CDF group names...
>
> 20150123 21:47:55| Reading CDF group names...done
>
> used (Mb) gc trigger (Mb) max used (Mb)
>
>Ncells 603933 32.3 899071 48.1 741108 39.6
>
>Vcells 1027587 7.91757946 13.5 1424724 10.9
>
> used (Mb) gc trigger (Mb) max used (Mb)
>
>Ncells 549349 29.4 899071 48.1 899071 48.1
>
>Vcells 945722 7.31757946 13.5 1424724 10.9
>
> 20150123 21:47:56| Number of cells per unit:
>
> Min. 1st Qu. MedianMean 3rd Qu.Max.
>
> 1 1 1 1 1 1
>
> 20150123 21:47:56| Reading CDF QC units...
>
> 20150123 21:47:56| Reading CDF QC units...done
>
> 20150123 21:47:56| Number of QC cells: 5385 in 9 QC units (0.1MB)
>
> 20150123 21:47:56| Total number of cells: 60060
>
> 20150123 21:47:56| Best array dimension: 246x245 (=60270 cells, i.e.
210 left-over cells)
>
> 20150123 21:47:56| Creating CDF header with source CDF as template...
>
> 20150123 21:47:56|Setting up header...
>
> 20150123 21:47:56| Reading CDF header...
>
> 20150123 21:47:56| Reading CDF header...done
>
> 20150123 21:47:56| Reading CDF unit names...
>
> 20150123 21:47:56| Reading CDF unit names...done
>
> 20150123 21:47:56|Setting up header...done
>
> 20150123 21:47:56|Writing...
>
> 20150123 21:47:56| destHeader:
>
> List of 12
>
> $ ncols : int 245
>
> $ nrows : int 246
>
> $ nunits : int 54675
>
> $ nqcunits : int 9
>
> $ refseq : chr ""
>
> $ chiptype : chr "HG-U133_Plus_2"
>
> $ filename : chr
"annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2.cdf"
>
> $ rows : int 1164
>
> $ cols : int 1164
>
> $ probesets : int 54675
>
> $ qcprobesets: int 9
>
> $ reference : chr ""
>
> 20150123 21:47:56| unitNames:
>
> chr [1:54675] "AFFX-BioB-5_at" "AFFX-BioB-M_at" "AFFX-BioB-3_at"
"AFFX-BioC-5_at" ...
>
> 20150123 21:47:56| qcUnitLengths:
>
> num [1:9] 15966 174 230 1658 69 ...
>
> 20150123 21:47:56| unitLengths:
>
> num [1:54675] 116 116 116 116 116 116 116 116 116 116 ...
>
>used (Mb) gc trigger (Mb) max used (Mb)
>
> Ncells 561416 30.0 984024 52.6 899071 48.1
>
> Vcells 1120064 8.61925843 14.7 1515846 11.6
>
>used (Mb) gc trigger (Mb) max used (Mb)
>
> Ncells 562232 30.1 984024 52.6 899071 48.1
>
> Vcells 1010995 7.85484388 41.9 6516658 49.8
>
> 20150123 21:47:57|Writing...done
>
> 20150123 21:47:57| Creating CDF header with source CDF as
template...done
>
> 20150123 21:47:57| Writing QC units...
>
> 20150123 21:47:57|
Re: [aroma.affymetrix] Questions on extracting probeset summaries
Thanks. I can *not* reproduce this, e.g.
> ces
ChipEffectSet:
Name: GSE9890
Tags: GRBC,QN,RMA,oligo
Path: plmData/GSE9890,GRBC,QN,RMA,oligo/HG-U133_Plus_2
Platform: Affymetrix
Chip type: HG-U133_Plus_2,monocell
Number of arrays: 10
Names: GSM249671, GSM249672, GSM249673, ..., GSM249680 [10]
Time period: 2015-01-17 09:43:28 -- 2015-01-17 09:43:35
Total file size: 5.75MB
RAM: 0.02MB
Parameters: {}
> ces[[1]]
ChipEffectFile:
Name: GSM249671
Tags: chipEffects
Full name: GSM249671,chipEffects
Pathname:
plmData/GSE9890,GRBC,QN,RMA,oligo/HG-U133_Plus_2/GSM249671,chipEffects.CEL
File size: 589.25 kB (603394 bytes)
RAM: 0.02 MB
File format: v4 (binary; XDA)
Platform: Affymetrix
Chip type: HG-U133_Plus_2,monocell
Timestamp: 2015-01-17 09:43:28
Parameters: {probeModel: chr "pm"}
> data <- extractDataFrame(ces, units=NULL, addNames=TRUE)
> str(data)
'data.frame': 54675 obs. of 15 variables:
$ unitName : chr "AFFX-BioB-5_at" "AFFX-BioB-M_at" "AFFX-BioB-3_at"
"AFFX-BioC-5_at" ...
$ groupName: chr "" "" "" "" ...
$ unit : int 1 2 3 4 5 6 7 8 9 10 ...
$ group: int 1 1 1 1 1 1 1 1 1 1 ...
$ cell : int 1 2 3 4 5 6 7 8 9 10 ...
$ GSM249671: num 1614 2691 2120 3904 2238 ...
$ GSM249672: num 2612 4060 3301 5686 3280 ...
$ GSM249673: num 2876 5178 4014 6861 4050 ...
$ GSM249674: num 3328 5704 4350 7617 4505 ...
$ GSM249675: num 3101 5455 4131 7735 4560 ...
$ GSM249676: num 5081 8883 7173 10997 7188 ...
$ GSM249677: num 2329 4186 3209 5853 3482 ...
$ GSM249678: num 1723 3177 2353 5537 3141 ...
$ GSM249679: num 1442 2458 2114 4285 2370 ...
$ GSM249680: num 1469 2641 2154 4583 2582 ...
So, let's start troubleshooting. First, you should see the exact same
as I do for:
> cdf <- getCdf(ces)
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/HG-U133_Plus_2
Filename: HG-U133_Plus_2,monocell.CDF
File size: 9.63 MB (10098009 bytes)
Chip type: HG-U133_Plus_2,monocell
RAM: 3.34MB
File format: v4 (binary; XDA)
Dimension: 246x245
Number of cells: 60270
Number of units: 54675
Cells per unit: 1.10
Number of QC units: 9
If not, that's where the problem is. If ok, then check this output:
> map <- getUnitGroupCellMap(cdf)
str(map)> str(map)
Classes 'UnitGroupCellMap' and 'data.frame':54675 obs. of 3 variables:
$ unit : int 1 2 3 4 5 6 7 8 9 10 ...
$ group: int 1 1 1 1 1 1 1 1 1 1 ...
$ cell : int 1 2 3 4 5 6 7 8 9 10 ...
This "map" is essential in what information gets pulled out and
returned. The number of rows/observations in this data frame should
match the number of units in the 'cdf', i.e. 54,675 units.
Let's start with that.
Henrik
On Thu, Jan 22, 2015 at 5:00 PM, Qingzhou Zhang wrote:
> Hi, Henrik,
>
> Thanks for the reply!
>
> Here is my code:
>
> library("aroma.affymetrix")
> RawName = "Project1"
> RawChipType = "HG-U133_Plus_2"
>
> ces <- doGCRMA(RawName, chipType = RawChipType)
> data <- extractDataFrame(ces, units = NULL, addNames = TRUE)
>
> Here is the sessionInfo()
>
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> LC_TIME=en_GB.UTF-8
> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_GB.UTF-8
> LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C
> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8
> LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] aroma.light_2.2.1 aroma.affymetrix_2.13.0 aroma.core_2.13.0
> R.devices_2.12.0
> [5] R.filesets_2.6.0R.utils_1.34.0 R.oo_1.18.2
> affxparser_1.38.0
> [9] R.methodsS3_1.6.2
>
> loaded via a namespace (and not attached):
> [1] aroma.apd_0.5.0base64enc_0.1-2Cairo_1.5-7digest_0.6.8
> DNAcopy_1.40.0
> [6] matrixStats_0.13.0 PSCBS_0.43.0 R.cache_0.11.0 R.huge_0.8.0
> R.rsp_0.19.7
> [11] tools_3.1.1
>
> Here is the traceback()
>
> 1: extractDataFrame(ces, units = NULL, addNames = TRUE)
>
>
> I tried several times, but always got a data frame containing 27604 obj. :-(
>
> Thanks
>
>
> On Friday, 23 January 2015 01:36:00 UTC+8, Henrik Bengtsson wrote:
>>
>> On Thu, Jan 22, 2015 at 5:44 AM, Qingzhou Zhang
>> wrote:
>> > Hi Henrik,
>> >
>> > I was processing HG-U133_Plus_2 datasets. While extracting probeset
>> > summaries(chip effects) as a data frame, I only got 27604 objs * n
>> > variables.
>> > I was hoping to get a data frame of 54675 objs., which equals the number
>>
[aroma.affymetrix] aroma.affymetrix v2.13.0 released
Hi,
aroma.affymetrix v2.13.0 and friends has been released and is now
available on CRAN for all the major operating systems. Intall/update
by:
source("http://callr.org/install#aroma.affymetrix";)
This will take care of all dependencies and recommended packages as
well (also those hosted on Bioconductor and elsewhere). BTW, you can
use this one-line approach to also install any CRAN and Bioconductor
packages out there.
What's new?
* Subsetting data sets and files is made more similar to how you work
with lists, e.g. ds[idxs] and ds[[idx]] works as expected. You can
safely stop using getFile(ds, idx) and use ds[[idx]] instead.
* `justRMA()` for AffymetrixCelSet replicates affx::justRMA(), but
does so with using much less memory allowing you to run 1000's of
arrays.
* As usal, bug fixes and robustness improvements (== you spend less
time troubleshooting and more time doing science). Although I keep
saying it, there's always ongoing work under the hood toward an
automagic parallel/distributed processing. It will happen one day.
Cheers,
Henrik
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Updates to aroma.affymetrix
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Version: 2.13.0 [2015-01-17]
o Bumped version for CRAN submission.
o Updated package dependencies.
o Package passes all redundancy tests.
Version: 2.12.10 [2015-01-06]
o CLEANUP: Major cleanup of namespace imports from suggested packages
such as affxparser and aroma.light.
Version: 2.12.9 [2014-11-17]
o Updated redundancy tests under testScripts/ to find rowMedians() of
the matrixStats package. The matrixStats package used to be attached
whenever aroma.light (< 2.1.1) was attached, but no longer.
Version: 2.12.8 [2014-09-04]
o ROBUSTNESS/BUG FIX: createFrom(..., mode="copy") for AffymetrixCelFile
would give an error on "No permission to modify existing file: ..."
iff the source file had read-only permission. This bug was introduced
by changes to base::file.copy() in R (>= 2.13.0) [April 2011].
Thanks to Taylor Raborn at Indiana University for reporting on this.
Version: 2.12.7 [2014-08-27]
o ROBUSTNESS: Added forgotten NAMESPACE imports.
Version: 2.12.6 [2014-06-29]
o BUG FIX: getAromaCellSequenceFile() for AffymetrixCdfFile used
undefined variable 'nbrOfCells'.
Version: 2.12.5 [2014-06-24]
o Added package system tests utilizing example data of Bioconductor
package AffymetrixDataTestFiles, iff installed.
Version: 2.12.4 [2014-06-09]
o Package now requires R (>= 3.0.0) and BioC (>= 2.13), which were
released April 2013 and are in fact old and it's recommended to
use a more recent version of R.
o Added 'SuggestsNote' field to DESCRIPTION with list of packages
that are recommended for the most common use cases.
o Bumped package dependencies.
Version: 2.12.3 [2014-05-02]
o CLEANUP: Now using ds[[idx]] instead of getFile(ds, idx) where possible.
Version: 2.12.2 [2014-04-28]
o Added justRMA() for AffymetrixCelSet, which with good precision
reproduces the results of the default setting of justRMA() in the
affy package. It does so by still running with a constant memory
profile. This means that a much larger number of samples can be
processed using this implementation.
o doCRMAv2(..., drop=FALSE) and hence doASCRMAv2(..., drop=FALSE), did
not *return* the base-position normalization step, although it was
done and its outcome was part of all downstream steps.
o extractExpressionSet() for ChipEffectSet gained argument 'orderUnitsBy'
and returns standard errors as well.
Version: 2.12.1 [2014-04-26]
o SPEEDUP: Minor speedup by replacing repetive ::() calls
with repetive () calls; the '::' operator is fairly expensive.
You should expect a small speed improvement when using MatSmoothing(),
RmaPlm(..., flavor="oligo") and when calculating weights using
ExonRmaPlm and QualityAssessmentModel, to name a few examples.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Updates to aroma.core
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Version: 2.13.0 [2015-01-07]
o Bumped version for CRAN submission.
o Updated package dependencies.
o Package passes all redundancy tests.
Version: 2.12.8 [2014-09-19]
o BUG FIX: display() for Explorer would try to open a pathname
in a way that only worked on Windows. Thanks to Sunghee Oh
(S. Korea) for reporting on this.
Version: 2.12.7 [2014-09-04]
o ROBUSTNESS: Wherever needed, files are now copied without preserving
file permissions (e.g. read-only), which became the default in
R (>= 2.13.0) [April 2013].
o Bumped package dependencies.
Version: 2.12.6 [2014-08-27]
o Now 'aromaSettings' are loaded when the packages is loaded.
Previously the package had to be attached.
o ROBUSTNESS: Now fit2d() for matrix utilizes use() for aroma.light.
o ROBUSTNESS: Added several missing NAMESPACE imports.
o BUG FIX: writeDataFrame(..., columnNamesPrefix="none") for
AromaUnitSignalBina
Re: [aroma.affymetrix] Re: Regarding the copy number states and further processing
Hi guys, here are some late feedback on this discussion: * When talking about copy numbers, it is important to always be very clear and distinguish between whether we talk about normal/germline CNs or tumor CNs. The former take integer CN levels (0, 1, 2, 3, ...), whereas for tumors we very rarely observe pure homogeneous tumor cells, which is why we only measure and observe non-integer CN levels. Hopefully, we observe at least discrete CN levels in tumors, but one should never expect integer levels. * aCGH: a historical term often used as a synonym for total copy numbers. For example, some say "aCGH analysis" when they really mean "total copy-number analysis". aCGH stands for array-CGH, or in full 'array comparative genomic hybridization'. This refers to the older generation two-color/two-channel arrays where a test and a reference sample where labelled with two different dyes and "competitively" hybridized to the same array and the same probes. I recommend to stop using this term and instead use "total copy number", total CN, or "TCN" (when it's clear). By being explicit about "total", you're also explicitly contrasting it to "parent-specific" CNs (which you can do if you have SNP data). * CNA: Copy-Number Aberration. This term can be applied to both tumor and germline samples. In tumors you expect non-integer CN levels. In germline/normals you expect integer CN levels (0, 1, 2, 3, ...). * CNP: Copy-Number Polymorphism. This term applies to copy-number differences in relationship to a population. This also implies we're talking about germline genomes. In other words, CNPs are also integer CN levels (0, 1, 2, 3, ...). CNPs are used to specify, say, "2% of the Europeans have a 1 copy deletion of length 1.0-1.5 Mb on Chr 3 at 124.5Mb". CNPs is for segment deletions and gains what SNPs are for nucleotide polymorphisms. The term CNP is rare. It is much more common to hear/see "CNV". * CNV: Copy-Number Variation. Ideally the word "variation" refers to "polymorphism" and therefore the term CNV should be used only to refer to CNPs. I don't know if there is a formal definitions, but I find it unfortunate to see CNV being used when CNA should be used. By my books, CNV only takes integer CN levels (0, 1, 2, 3, ...). The term CNV should never be used to refer to CN levels in tumors. * Calling total CN levels is very hard in tumors, and as the first above point alludes to, it may not even be a well defined problem. For instance, imagine you have a tumor sample with 5% tumor cells and 95% normal cells, and that the those tumors cells all have a deletion on Chr 2. Then, at what point to you consider that sample itself to have a deletion on Chr 2? Are you after he sample/tissue itself, or are you after those 5% tumors cells? What if you have a heterogeneous mix of tumor cells? The more precise you can specify your question the more easy it is for you to decided what approach forward (may) work and what doesn't work. Here "work" can also be read as "make sense". * The first and most important task for almost all segmentation methods is to *segment* the genome, that is, identify at what genomic locations the observed DNA (tumor, normal or a mix) changes in CN level. Together, these location, aka "change points", defines how the genome can be "partitioned" into segments with equal CN levels, such that when we look at a particular segment, we can assume that all genomic locations within that segment has the same underlying genomic composition (e.g. gain, loss, loss in 5% of the cells, etc.). CBS, GLAD, and many other methods, segment the genome this way as a first step. * A common task after having decided on the segments (partitioning of the genome), is to decide on what is going on within each segment. Not all methods does this. For instance, CBS "only" provides you with the change points. GLAD on the other hand does both the segmentation and then also provides a method for calling. Theoretically, there is nothing preventing you from using the GLAD *calling* algorithm using the segmentation found by CBS. Unfortunately, I don't think it is straightforward to do that in practice; at least you have to coerce one data format into one that GLAD understands. * GLAD does not scale well with the number of loci, because it's computational complexity is ~O(n^2), unless things have changed since. In 2007, I tried to predict GLAD's processing time when we were using the Affymetrix 500K chips and the GenomeWideSNP_5 and GenomeWideSNP_6 were starting to come out. A GWS6 chip would basically take days to segment. See attached PNG for a table. * CBS is much faster as an algorithm. Also, the implementation in the DNAcopy package has been made even faster over time. There was a major speedup back in 2009, cf. http://aroma-project.org/benchmarks/DNAcopy_v1.19.2-speedup/ Over and for now Henrik On Thu, Jan 22, 2015 at 12:42 AM, Chengyu Liu wrote: > Hi, > >> >> I have tried this and works goo
Re: [aroma.affymetrix] Questions on extracting probeset summaries
On Thu, Jan 22, 2015 at 5:44 AM, Qingzhou Zhang wrote: > Hi Henrik, > > I was processing HG-U133_Plus_2 datasets. While extracting probeset > summaries(chip effects) as a data frame, I only got 27604 objs * n > variables. > I was hoping to get a data frame of 54675 objs., which equals the number of > units in HG-U133_Plus_2 chip. Am I missing some steps, or processing the > wrong CEL files? Hard to say. Can you share your code (from beginning to end) showing what you're doing? Henrik > > Thanks a lot! > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] sfit
It seems as you don't have the 'sfit' package installed. Not sure how
you installed aroma.affymetrix in the first place (the recommended way
is shown at http://aroma-project.org/install/), but try:
source('http://callr.org/install#sfit')
That should install 'sfit'. If the installation of 'sfit' fails/gives
an error, please report the error along with your version of R and
operating system.
/Henrik
On Wed, Jan 21, 2015 at 5:46 AM, Juanjo Lozano
wrote:
> Hi,
>
> I found
>
> Error: Package not loaded: sfit
> Execution halted
>
> in
>
> R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
>
> Could you help-me?
>
> Best
>
> Juanjo
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> ---
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to aroma-affymetrix+unsubscr...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
---
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To unsubscribe from this group and stop receiving emails from it, send an email
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For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] Is it necessary to update annotation files (CytoscanHD array)
Hi. The Aroma Cell Sequence (ACS) file does not have to be updated, since it only contains the probe sequences on the array and those never changes. The Unit Genome Position (UGP) file specifies the (chr, pos) genomic coordinates for the probe sets, which depends on the genome reference/build. Likewise, the Unit Fragment Length (UFL) file specify the PCR fragment lengths as cut by the restriction enzyme (part of the Affymetrix assay). These cut locations also depend on the genome reference/build. So, yes, UGP and UFL files needs to match the genome build wanted. (However, I wouldn't expect much any major/noticeable difference in CN estimates if not perfect version matching since not too much have changed and most discrepancies would come through as a few number outliers). To build newer versions yourself, please see how-to docs: * Create a Unit Genome Position (UGP) files * Create a Unit Fragment Length (UFL) files available via http://aroma-project.org/howtos/ Hope this helps Henrik On Thu, Jan 8, 2015 at 5:44 AM, Chengyu Liu wrote: > Hi, > > Is it necessary to update annotation files in > http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/. > It is quite old. Or I can use them without update. > > Br, > C.Y > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] Could not loacate CystoScanHD_Array annotation
On Jan 7, 2015 3:43 AM, "Chengyu Liu" wrote:
>
> Thanks，it is working now. I am sorry for the late reply. I was on
holidays and just back.
> About ACS, UGP and UFL, are they necessary for the copy number calls?
Yes.
Henrik
>
> Br,
>
>
> On Monday, December 15, 2014 8:25:17 PM UTC+2, Henrik Bengtsson wrote:
>>
>> On Mon, Dec 15, 2014 at 8:38 AM, Chengyu Liu
wrote:
>> > Thanks.
>> >
>> > I tried to bypass the NetAffx issue. I downloaded the cdf file from
aroma
>> > (
http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/)
>> > and Affymetrix website.
>> > Annotation file can be located, but following functions does not work.
It
>> > was my first time to deal with aroma.afymetrix package. Maybe I was
using
>> > wrong way.
>>
>> Regarding this one: Download (and gunzip) also the ACS, UGP and UFL
>> files and place them in annotationData/chipTypes/CytoScanHD_Array/ and
>> then the following will work.
>>
>> /Henrik
>>
>> >
>> > Any comments are appreciated.
>> >
>> >> cdf <- AffymetrixCdfFile$byChipType('CytoScanHD_Array');
>> >> print(cdf)
>> > AffymetrixCdfFile:
>> > Path: annotationData/chipTypes/CytoScanHD_Array
>> > Filename: CytoScanHD_Array.cdf
>> > File size: 612.27 MB (642007896 bytes)
>> > Chip type: CytoScanHD_Array
>> > RAM: 0.00MB
>> > File format: v4 (binary; XDA)
>> > Dimension: 2572x2680
>> > Number of cells: 6892960
>> > Number of units: 2822125
>> > Cells per unit: 2.44
>> > Number of QC units: 4
>> >
>> >>gi <- getGenomeInformation(cdf)
>> > [2014-12-15 18:28:32] Exception: Failed to retrieve genome information
for
>> > this chip type: CytoScanHD_Array
>> >
>> > at #02. getGenomeInformation.AffymetrixCdfFile(cdf)
>> > - getGenomeInformation.AffymetrixCdfFile() is in environment
>> > 'aroma.affymetrix'
>> >
>> > at #01. getGenomeInformation(cdf)
>> > - getGenomeInformation() is in environment
'aroma.affymetrix'
>> >
>> > Error: Failed to retrieve genome information for this chip type:
>> > CytoScanHD_Array
>> >
>> >>si <- getSnpInformation(cdf)
>> > 20141215 18:31:41|Defining DChipSnpInformation from chip type...
>> > 20141215 18:31:41| Chip type: CytoScanHD_Array
>> > 20141215 18:31:41| Version:
>> > 20141215 18:31:41| Located pathname:
>> > 20141215 18:31:41|Defining DChipSnpInformation from chip type...done
>> > [2014-12-15 18:31:41] Exception: Failed to retrieve SNP information
for this
>> > chip type: CytoScanHD_Array
>> >
>> > at #02. getSnpInformation.AffymetrixCdfFile(cdf)
>> > - getSnpInformation.AffymetrixCdfFile() is in environment
>> > 'aroma.affymetrix'
>> >
>> > at #01. getSnpInformation(cdf)
>> > - getSnpInformation() is in environment 'aroma.affymetrix'
>> >
>> > Error: Failed to retrieve SNP information for this chip type:
>> > CytoScanHD_Array
>> >
>> >>acs <- AromaCellSequenceFile$byChipType(getChipType(cdf,
fullname=FALSE))
>> > [2014-12-15 18:31:50] Exception: Failed to create
AromaCellSequenceFile
>> > object. Could not locate an annotation data file for chip type
>> > 'CytoScanHD_Array' (without requiring any tags) and with filename
extension
>> > 'acs'.
>> >
>> > at #03. byChipType.AromaMicroarrayTabularBinaryFile(static, ...)
>> > - byChipType.AromaMicroarrayTabularBinaryFile() is in
environment
>> > 'aroma.core'
>> >
>> > at #02. byChipType(static, ...)
>> > - byChipType() is in environment 'aroma.core'
>> > - originating from ''
>> >
>> > at #01. AromaCellSequenceFile$byChipType(getChipType(cdf, fullname =
>> > FALSE))
>> > - AromaCellSequenceFile$byChipType() is local of the calling
>> > function
>> >
>> > Error: Failed to create AromaCellSequenceFile object. Could not locate
an
>> > annotation data file for chip type 'CytoScanHD_Array' (without
requiring any
>> > tags) and with filename extension 'acs'.
>> >
>> >
>> > On Monday, December 15, 2014 6:27:51 PM UTC+2, Henrik Bengtsson wrote:
>> >>
>> >> I can reproduce this;
>> >&g
Re: [aroma.affymetrix] RmaBackgroundCorrection: error on v4-to-v3-converted HuEx-1_0-st-v2 CEL file
On Jan 3, 2015 2:54 AM, "Amon" wrote:
>
> Hi Henrik,
>
> Thanks for the tip; I did try clearing the cache as you suggested as well
as running it on --vanilla but the same error appeared. In the interests of
saving time, I've rerun the whole process on my personal laptop, which has
an up-to-date version of R (I used an external server previously, so no
admin privileges), and it ran without any problems... so that was probably
the issue.
Good to hear.
It's still weird to me because weekly redundancy test on exactly this is
known to have worked for years without issues. I would blame neither R nor
affxparser but some random hiccup during installation on that particular
machine.
You might f find it useful to know that you can install R from source on
user accounts with very little privileges ... and it's fairly easy if the
compilers are up to date.
Henrik
>
> Many thanks again.
>
> Aisyah
>
> On Saturday, January 3, 2015 7:53:13 AM UTC+8, Henrik Bengtsson wrote:
>>
>> I fail to reproduce this with R 3.0.2 and affxparser 1.34.4 and
>> aroma.affymetrix_2.12.8 and the same data file (just like you).
>>
>> However, from code inspection it could be that you have some cached
>> results from an earlier run that used a CDF with the exact same
>> filename but with an actually different content - could that be the
>> case? (I'll try to close that pitfall in the next release). If this
>> is the problem, then try to clear your cache. The content in
>> ~/.Rcache/ is non-critical and can be deleted at any time. You can
>> erase the cache like this:
>>
>> > library("R.cache")
>> > clearCache()
>> Are you really sure you want to delete the 184 files and 16
>> directories in '/home/JohnDoe/.Rcache'? [y/N]: y
>>
>> The only thing you'll notice is that some steps will be slow when you
>> run the first time after clearing the cache. This is the Aroma
>> Framework recalculating/regenerated part of the cache.
>>
>> Let me know if this works. If not, other ideas are:
>>
>> * You seem to have other packages loaded/attached too. Retry in a
>> fresh R session, e.g. R --vanilla.
>>
>> * Your R version and therefore your affxparser versions are outdated.
>> I would retry with a recent version of R, i.e. R >= 3.1.2.
>>
>> /Henrik
>>
>>
>> On Mon, Dec 29, 2014 at 5:20 PM, Amon wrote:
>> > Below is the output (for the binary, not text, CEL file) :
>> >
>> >> cf <- cs[[1]]
>> >> print(cf) # Should be the 'EA_BT549' CEL file
>> > AffymetrixCelFile:
>> > Name: EA_BT549
>> > Tags:
>> > Full name: EA_BT549
>> > Pathname: rawData/myData/HuEx-1_0-st-v2/EA_BT549.CEL
>> > File size: 63.16 MB (66226783 bytes)
>> > RAM: 0.01 MB
>> > File format: v4 (binary; XDA)
>> > Platform: Affymetrix
>> > Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
>> > Timestamp: 2007-08-30 20:27:52
>> >> str(getHeader(cf))
>> > List of 14
>> > $ filename : chr "rawData/myData/HuEx-1_0-st-v2/EA_BT549.CEL"
>> > $ version : int 4
>> > $ cols : int 2560
>> > $ rows : int 2560
>> > $ total : int 6553600
>> > $ algorithm : chr "Percentile"
>> > $ parameters: chr
>> >
"Percentile:75;CellMargin:4;OutlierHigh:1.500;OutlierLow:1.004;AlgVersion:6.0;FixedCellSize:TRUE;FullFeatureWidth:7;FullFeatureH"|
>> > __truncated__
>> > $ chiptype : chr "HuEx-1_0-st-v2"
>> > $ header: chr
>> >
"Cols=2560\nRows=2560\nTotalX=2560\nTotalY=2560\nOffsetX=0\nOffsetY=0\nGridCornerUL=617
>> > 453\nGridCornerUR=18881 579\nGridCornerL"| __truncated__
>> > $ datheader : chr "[0..65534] 0293_BT549:CLS=19341RWS=19341XIN=0
>> > YIN=0 VE=302.0 08/30/07 20:27:52 54716690 M10 \024 \024
>> > HuEx-1_0-s"| __truncated__
>> > $ librarypackage: chr ""
>> > $ cellmargin: int 4
>> > $ noutliers : int 172409
>> > $ nmasked : int 0
>> >
>> >
>> > If it helps for you to visually inspect the file yourself, I
downloaded this
>> > file from a publicly available dataset here
>> > http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-181/samples/
BT549 is
>> > the 8th row from the top I think.
>> >
>> > Best
>> >
>> > Aisyah
>> >
>> > On Tuesday, December 30, 2014 9:11:26 AM UTC+8, Henrik Bengtsson
wro
Re: [aroma.affymetrix] RmaBackgroundCorrection: error on v4-to-v3-converted HuEx-1_0-st-v2 CEL file
I fail to reproduce this with R 3.0.2 and affxparser 1.34.4 and
aroma.affymetrix_2.12.8 and the same data file (just like you).
However, from code inspection it could be that you have some cached
results from an earlier run that used a CDF with the exact same
filename but with an actually different content - could that be the
case? (I'll try to close that pitfall in the next release). If this
is the problem, then try to clear your cache. The content in
~/.Rcache/ is non-critical and can be deleted at any time. You can
erase the cache like this:
> library("R.cache")
> clearCache()
Are you really sure you want to delete the 184 files and 16
directories in '/home/JohnDoe/.Rcache'? [y/N]: y
The only thing you'll notice is that some steps will be slow when you
run the first time after clearing the cache. This is the Aroma
Framework recalculating/regenerated part of the cache.
Let me know if this works. If not, other ideas are:
* You seem to have other packages loaded/attached too. Retry in a
fresh R session, e.g. R --vanilla.
* Your R version and therefore your affxparser versions are outdated.
I would retry with a recent version of R, i.e. R >= 3.1.2.
/Henrik
On Mon, Dec 29, 2014 at 5:20 PM, Amon wrote:
> Below is the output (for the binary, not text, CEL file) :
>
>> cf <- cs[[1]]
>> print(cf) # Should be the 'EA_BT549' CEL file
> AffymetrixCelFile:
> Name: EA_BT549
> Tags:
> Full name: EA_BT549
> Pathname: rawData/myData/HuEx-1_0-st-v2/EA_BT549.CEL
> File size: 63.16 MB (66226783 bytes)
> RAM: 0.01 MB
> File format: v4 (binary; XDA)
> Platform: Affymetrix
> Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
> Timestamp: 2007-08-30 20:27:52
>> str(getHeader(cf))
> List of 14
> $ filename : chr "rawData/myData/HuEx-1_0-st-v2/EA_BT549.CEL"
> $ version : int 4
> $ cols : int 2560
> $ rows : int 2560
> $ total : int 6553600
> $ algorithm : chr "Percentile"
> $ parameters: chr
> "Percentile:75;CellMargin:4;OutlierHigh:1.500;OutlierLow:1.004;AlgVersion:6.0;FixedCellSize:TRUE;FullFeatureWidth:7;FullFeatureH"|
> __truncated__
> $ chiptype : chr "HuEx-1_0-st-v2"
> $ header: chr
> "Cols=2560\nRows=2560\nTotalX=2560\nTotalY=2560\nOffsetX=0\nOffsetY=0\nGridCornerUL=617
> 453\nGridCornerUR=18881 579\nGridCornerL"| __truncated__
> $ datheader : chr "[0..65534] 0293_BT549:CLS=19341RWS=19341XIN=0
> YIN=0 VE=302.0 08/30/07 20:27:52 54716690 M10 \024 \024
> HuEx-1_0-s"| __truncated__
> $ librarypackage: chr ""
> $ cellmargin: int 4
> $ noutliers : int 172409
> $ nmasked : int 0
>
>
> If it helps for you to visually inspect the file yourself, I downloaded this
> file from a publicly available dataset here
> http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-181/samples/ BT549 is
> the 8th row from the top I think.
>
> Best
>
> Aisyah
>
> On Tuesday, December 30, 2014 9:11:26 AM UTC+8, Henrik Bengtsson wrote:
>>
>> It turns out this error is triggered inside affxparser::updateCel()
>> and it looks like it can happen for two reasons, where one is due to a
>> corrupt/corruptly read CEL header. What does
>>
>> > cdf <- AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2",
>> > tags="fullR3,A20071112,EP")
>> > cs <- AffymetrixCelSet$byName("myData", cdf=cdf)
>> > cf <- cs[[1]]
>> > print(cf) # Should be the 'EA_BT549' CEL file
>> > str(getHeader(cf))
>>
>> output?
>>
>> /Henrik
>>
>>
>> On Mon, Dec 29, 2014 at 4:39 PM, Amon wrote:
>> > Hi Henrik, thanks for your very prompt response. Below is the error
>> > message
>> > I got when I tried to run the same code on the unconverted (i.e.,
>> > original)
>> > v4 CEL file. I've reddened the area that alerted me to the possibility
>> > that
>> > it's the format of the file that caused it not to work (the binary
>> > format
>> > possibly causes NA values, creating the "missing value where TRUE/FALSE
>> > needed" error), because as I said I've run this preprocessing step on my
>> > v3
>> > data, using the same CDF, many times with no problems before:
>> >
>> > 20141229 05:17:51|Background correcting data set...
>> > 20141229 05:17:51| Number of arrays: 1
>> > 20141229 05:17:51| Array #1 ('EA_BT549') of 1...
>> > 20141229 05:17:52| Adjusting PM signals only
>> > 20141229 05:17:52| Obtaining signals...
>> > 20141229 05:17:53| Ob
Re: [aroma.affymetrix] RmaBackgroundCorrection: error on v4-to-v3-converted HuEx-1_0-st-v2 CEL file
It turns out this error is triggered inside affxparser::updateCel()
and it looks like it can happen for two reasons, where one is due to a
corrupt/corruptly read CEL header. What does
> cdf <- AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2",
> tags="fullR3,A20071112,EP")
> cs <- AffymetrixCelSet$byName("myData", cdf=cdf)
> cf <- cs[[1]]
> print(cf) # Should be the 'EA_BT549' CEL file
> str(getHeader(cf))
output?
/Henrik
On Mon, Dec 29, 2014 at 4:39 PM, Amon wrote:
> Hi Henrik, thanks for your very prompt response. Below is the error message
> I got when I tried to run the same code on the unconverted (i.e., original)
> v4 CEL file. I've reddened the area that alerted me to the possibility that
> it's the format of the file that caused it not to work (the binary format
> possibly causes NA values, creating the "missing value where TRUE/FALSE
> needed" error), because as I said I've run this preprocessing step on my v3
> data, using the same CDF, many times with no problems before:
>
> 20141229 05:17:51|Background correcting data set...
> 20141229 05:17:51| Number of arrays: 1
> 20141229 05:17:51| Array #1 ('EA_BT549') of 1...
> 20141229 05:17:52| Adjusting PM signals only
> 20141229 05:17:52| Obtaining signals...
> 20141229 05:17:53| Obtaining signals...done
> 20141229 05:17:53| Applying normal+exponential signal model...
> 20141229 05:17:55| Applying normal+exponential signal model...done
> 20141229 05:17:55| Writing adjusted probe signals...
> 20141229 05:17:55| Adding temporary suffix from file...
> 20141229 05:17:55|Pathname:
> probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL
> 20141229 05:17:55|Suffix: .tmp
> 20141229 05:17:55|Rename existing file?: FALSE
> 20141229 05:17:55|Temporary pathname:
> probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp
> 20141229 05:17:55| Adding temporary suffix from file...done
> 20141229 05:17:55| Creating CEL file for results, if missing...
> 20141229 05:17:55|Creating CEL file...
> 20141229 05:17:55| Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
> 20141229 05:17:55| Pathname:
> probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp
> 20141229 05:17:55| Adding temporary suffix from file...
> 20141229 05:17:55| Pathname:
> probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp
> 20141229 05:17:55| Suffix: .tmp
> 20141229 05:17:55| Rename existing file?: FALSE
> 20141229 05:17:55| Temporary pathname:
> probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp.tmp
> 20141229 05:17:55| Adding temporary suffix from file...done
> 20141229 05:17:55| Method 'copy'...
> 20141229 05:17:55| Copying file safely...
> 20141229 05:17:55| Source: rawData/myData/HuEx-1_0-st-v2/EA_BT549.CEL
> 20141229 05:17:55| Destination:
> probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp.tmp
> 20141229 05:17:55| Copying to temporary file using file.copy()...
> 20141229 05:17:57| Copying to temporary file using file.copy()...done
> 20141229 05:17:57| Renaming temporary file to destination name...
> 20141229 05:17:57| Renaming temporary file to destination name...done
> 20141229 05:17:57| Validating destination file...
> 20141229 05:17:57| Validating destination file...done
> 20141229 05:17:57| Copying file safely...done
> 20141229 05:17:57| Renaming AffymetrixCelFile pathname...
> 20141229 05:17:57| Source:
> probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp.tmp
> 20141229 05:17:57| Destination:
> probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp
> 20141229 05:17:57| Renaming file...
> 20141229 05:17:57| Renaming file...done
> 20141229 05:17:57| Renaming AffymetrixCelFile pathname...done
> 20141229 05:17:57| Method 'copy'...done
> AffymetrixCelFile:
> Name: EA_BT549.CEL.tmp
> Tags:
> Full name: EA_BT549.CEL.tmp
> Pathname: probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp
> File size: 63.16 MB (66226783 bytes)
> RAM: 0.00 MB
> File format: v4 (binary; XDA)
> Platform: Affymetrix
> Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
> Timestamp: 2007-08-30 20:27:52
> 20141229 05:17:58|Creating CEL file...done
> 20141229 05:17:58| Creating CEL file for results, if missing...done
> 20141229 05:17:58| Writing adjusted intensities...
> Error in if (r[1] < 1 || r[2] > nbrOfCells) { :
> missing value where TRUE/FALSE needed
> 20141229 05:17:59| Writing adjusted intensities...done
> 20141229 05:17:59| Writing adjusted probe signals...done
> 20141229 05:17:59| Array #1 ('EA_BT549') of 1...done
> 201412
Re: [aroma.affymetrix] RmaBackgroundCorrection: error on v4-to-v3-converted HuEx-1_0-st-v2 CEL file
On Mon, Dec 29, 2014 at 1:37 PM, Amon wrote:
> Hello,
>
> I'd like to perform background correction on a HuEx-1_0-st-v2 CEL file that
> I've previously converted from xda binary format (Affymetrix v4) to ASCII
> text format (Affymetrix v3). I did the file format conversion because aroma
> does not work xda-format CEL files,
This is not correct. Where did you read this (because if it's written
somewhere it should be corrected)?
The aroma.affymetrix package works with the binary/XDA CEL file format
too. From the front page of http://aroma-project.org/:
"File formats: Works directly with CEL and CDF files (all versions;
text/ASCII, binary/XDA, binary/Calvin)."
It's unnecessary to convert back to ASCII and it would also slow things down.
I would retry with the binary/XDA CEL files and see if you still get
the error. If so, I'll look into it. If the error only occurs with
ASCII CEL files, I'll add it to the to do list to troubleshoot.
Hope this helps
Henrik
> and I used apt-cel-convert provided by
> Affymetrix Power Tools for this conversion. There are several error messages
> that come up when I use RmaBackgroundCorrection() on the file, some of which
> are:
>
> 20141229 20:59:04| Cannot create CEL file of version 4
> (probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp). Template CEL file is
> of version 3: rawData/myData/HuEx-1_0-st-v2/EA_BT549.CEL
> 20141229 21:00:50| Method 'create'...done
> AffymetrixCelFile:
> Name: EA_BT549.CEL.tmp
> Tags:
> Full name: EA_BT549.CEL.tmp
> Pathname: probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp
> File size: 62.50 MB (65536700 bytes)
> RAM: 0.00 MB
> File format: v4 (binary; XDA)
> Platform: Affymetrix
> Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
> Timestamp: 2014-12-29 20:59:04
> 20141229 21:00:51|Creating CEL file...done
> 20141229 21:00:51| Creating CEL file for results, if missing...done
> 20141229 21:00:51| Writing adjusted intensities...
> Error in if (r[1] < 1 || r[2] > nbrOfCells) { :
> missing value where TRUE/FALSE needed
> 20141229 21:00:51| Writing adjusted intensities...done
> 20141229 21:00:51| Writing adjusted probe signals...done
> 20141229 21:00:51| Array #1 ('EA_BT549') of 1...done
> 20141229 21:00:51|Background correcting data set...done
>
> I've provided the full report of the process in the attachment. From the
> error message, it seems that the information from the original v4 file has
> been retained somehow. Is there an option I can use in the
> RmaBackgroundCorrection() function to fix this? Steps I used prior to this
> were those found in the aroma page (additionally, I've used this on my v3
> data many times before with no problems):
>
> chipType <- "HuEx-1_0-st-v2"
> cdf <- AffymetrixCdfFile$byChipType(chipType, tags = "fullR3,A20071112,EP")
> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> cs <- AffymetrixCelSet$byName("myData", cdf=cdf)
> bc <- RmaBackgroundCorrection(cs)
> csBC <- process(bc, verbose = verbose)
>
> -
>
>> sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] splines grid parallel stats graphics grDevices utils
> datasets methods base
>
> other attached packages:
> [1] Hmisc_3.14-6Formula_1.1-2 survival_2.37-7
> lattice_0.20-29 aroma.light_2.0.0
> [6] matrixStats_0.10.0 aroma.affymetrix_2.12.8 aroma.core_2.12.8
> R.devices_2.12.0R.filesets_2.6.0
> [11] affy_1.40.0 Biobase_2.22.0 BiocGenerics_0.8.0
> affxparser_1.34.2 R.utils_1.34.0
> [16] R.oo_1.18.2 R.methodsS3_1.6.2
>
> loaded via a namespace (and not attached):
> [1] BiocInstaller_1.12.1 DNAcopy_1.36.0PSCBS_0.43.0
> R.cache_0.11.0R.huge_0.8.0 R.rsp_0.19.6
> [7] RColorBrewer_1.1-2acepack_1.3-3.3 affyio_1.30.0
> aroma.apd_0.5.0 base64enc_0.1-2 cluster_1.15.3
> [13] digest_0.6.7 foreign_0.8-61latticeExtra_0.6-26
> nnet_7.3-8preprocessCore_1.24.0 rpart_4.1-8
> [19] tools_3.0.2 zlibbioc_1.8.0
>
>
>
> Many thanks in advance.
>
> Aish
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
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>
> ---
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> email to aroma-affym
Re: [aroma.affymetrix] Encountered ERROR while extracting chip effects
On Thu, Dec 11, 2014 at 4:52 AM, Rishi Das Roy wrote:
> Hi
>
> Thanks for your reply. I can understand that I can identify alternative
> splicing through FIRMA more confidently. However I also want to identify
> differentially expressed genes. I have not find any documentation regarding
> this in aroma-project.org .
>
> Please provide any example to find DE genes through aroma.affymetrix.
If you look at http://aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis,
you find the following passages:
"There are two options, regardless of the kind of custom CDF you use.
To fit a summary of the entire transcript (i.e. estimate the overall
expression for the transcript), do:
plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)
print(plmTr)
and then a bit later also:
To extract the estimates (transcript or probeset) use either
extractMatrix() or extractDataFrame() on the ChipEffectSet that
corresponds to the plm object:
cesTr <- getChipEffectSet(plmTr)
trFit <- extractDataFrame(cesTr, units=1:3, addNames=TRUE)
This will give a data.frame with three rows, each row corresponding to
a unit/transcript."
Hope this helps
Henrik
>
> Thanks
> rishi
>
>
>
> On Wednesday, December 10, 2014 11:39:50 PM UTC+2, Henrik Bengtsson wrote:
>>
>> Hi,
>>
>> you cannot use RMA on exon-arrays, you will need to use exon-aware
>> method such as FIRMA (e.g.
>> http://aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis).
>>
>> Hope this helps
>>
>> Henrik
>>
>> PS. For http://aroma-project.org/replication/RMA, I've updated it to
>> use `theta <- extractTheta(ces)` instead of `theta <-
>> extractMatrix(ces)`. This will allow you to set the row names. But
>> as you'll find out, 'theta' becomes an JxKxI array for exon-arrays,
>> where J is the number of genes, I is the number of samples and K is
>> the maximum number of exons per gene found. In other words, using
>> doRMA() on exon arrays gives you at best exon-specific estimates (and
>> they are not very good estimates - FIRMA is doing a much better job on
>> that).
>>
>>
>>
>> On Wed, Dec 10, 2014 at 1:51 AM, Rishi Das Roy
>> wrote:
>> > Hi,
>> >
>> > I was trying to perform RMA on Mouse Exon 1.0 ST Array as described in
>> > aroma
>> > website (link) using custom cdf
>> > MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf.gz .
>> >
>> > I have executed following code in R
>> >
>> > cdf <- AffymetrixCdfFile$byChipType(chipType,
>> > tags="coreR1,A20080718,MR")
>> > cs <- AffymetrixCelSet$byName("data_CEL", cdf=cdf);
>> > bc <- RmaBackgroundCorrection(cs);
>> > csB <- process(bc);
>> > qn <- QuantileNormalization(csB, typesToUpdate="pm");
>> > csN <- process(qn);
>> > plm <- RmaPlm(csN);
>> > fit(plm);
>> > ces <- getChipEffectSet(plm);
>> > theta <- extractMatrix(ces);
>> > rownames(theta) <- getUnitNames(cdf);
>> > Error in `rownames<-`(`*tmp*`, value = c("6838637", "6992377",
>> > "6901592", :
>> > length of 'dimnames' [1] not equal to array extent
>> >
>> > Please help me to understand this error and how can I solve this. The
>> > session info is given below.
>> >
>> > With regards
>> > Rishi
>> >
>> > R version 3.1.2 (2014-10-31)
>> > Platform: x86_64-pc-linux-gnu (64-bit)
>> >
>> > locale:
>> > [1] LC_CTYPE=fi_FI.UTF-8LC_NUMERIC=CLC_TIME=en_GB
>> > LC_COLLATE=en_GBLC_MONETARY=fi_FI.UTF-8
>> > [6] LC_MESSAGES=en_GB LC_PAPER=en_GB LC_NAME=C
>> > LC_ADDRESS=CLC_TELEPHONE=C
>> > [11] LC_MEASUREMENT=en_GBLC_IDENTIFICATION=C
>> >
>> > attached base packages:
>> > [1] stats4parallel stats graphics grDevices utils datasets
>> > methods base
>> >
>> > other attached packages:
>> > [1] preprocessCore_1.28.0 aroma.light_2.2.0
>> > aroma.affymetrix_2.12.8 aroma.core_2.12.8
>> > [5] R.devices_2.12.0 R.filesets_2.6.0
>> > R.utils_1.34.0R.oo_1.18.2
>> > [9] R.methodsS3_1.6.2 affxparser_1.38.0
>> > pd.moex10st.mm.aceviewg_0.0.1 affy_1.44.0
>> > [13] BiocInstaller_1.16.1 pd.moex.1.0.st.v1_3.10.0
>> > RSQLite_1.0.0 DBI_0.3.1
>> > [17] moex10stmmrefseqcdf_19.0.0AnnotationDbi_1.28.1
>> > GenomeIn
Re: [aroma.affymetrix] Could not loacate CystoScanHD_Array annotation
On Mon, Dec 15, 2014 at 8:38 AM, Chengyu Liu wrote:
> Thanks.
>
> I tried to bypass the NetAffx issue. I downloaded the cdf file from aroma
> (http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/)
> and Affymetrix website.
> Annotation file can be located, but following functions does not work. It
> was my first time to deal with aroma.afymetrix package. Maybe I was using
> wrong way.
Regarding this one: Download (and gunzip) also the ACS, UGP and UFL
files and place them in annotationData/chipTypes/CytoScanHD_Array/ and
then the following will work.
/Henrik
>
> Any comments are appreciated.
>
>> cdf <- AffymetrixCdfFile$byChipType('CytoScanHD_Array');
>> print(cdf)
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/CytoScanHD_Array
> Filename: CytoScanHD_Array.cdf
> File size: 612.27 MB (642007896 bytes)
> Chip type: CytoScanHD_Array
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2572x2680
> Number of cells: 6892960
> Number of units: 2822125
> Cells per unit: 2.44
> Number of QC units: 4
>
>>gi <- getGenomeInformation(cdf)
> [2014-12-15 18:28:32] Exception: Failed to retrieve genome information for
> this chip type: CytoScanHD_Array
>
> at #02. getGenomeInformation.AffymetrixCdfFile(cdf)
> - getGenomeInformation.AffymetrixCdfFile() is in environment
> 'aroma.affymetrix'
>
> at #01. getGenomeInformation(cdf)
> - getGenomeInformation() is in environment 'aroma.affymetrix'
>
> Error: Failed to retrieve genome information for this chip type:
> CytoScanHD_Array
>
>>si <- getSnpInformation(cdf)
> 20141215 18:31:41|Defining DChipSnpInformation from chip type...
> 20141215 18:31:41| Chip type: CytoScanHD_Array
> 20141215 18:31:41| Version:
> 20141215 18:31:41| Located pathname:
> 20141215 18:31:41|Defining DChipSnpInformation from chip type...done
> [2014-12-15 18:31:41] Exception: Failed to retrieve SNP information for this
> chip type: CytoScanHD_Array
>
> at #02. getSnpInformation.AffymetrixCdfFile(cdf)
> - getSnpInformation.AffymetrixCdfFile() is in environment
> 'aroma.affymetrix'
>
> at #01. getSnpInformation(cdf)
> - getSnpInformation() is in environment 'aroma.affymetrix'
>
> Error: Failed to retrieve SNP information for this chip type:
> CytoScanHD_Array
>
>>acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
> [2014-12-15 18:31:50] Exception: Failed to create AromaCellSequenceFile
> object. Could not locate an annotation data file for chip type
> 'CytoScanHD_Array' (without requiring any tags) and with filename extension
> 'acs'.
>
> at #03. byChipType.AromaMicroarrayTabularBinaryFile(static, ...)
> - byChipType.AromaMicroarrayTabularBinaryFile() is in environment
> 'aroma.core'
>
> at #02. byChipType(static, ...)
> - byChipType() is in environment 'aroma.core'
> - originating from ''
>
> at #01. AromaCellSequenceFile$byChipType(getChipType(cdf, fullname =
> FALSE))
> - AromaCellSequenceFile$byChipType() is local of the calling
> function
>
> Error: Failed to create AromaCellSequenceFile object. Could not locate an
> annotation data file for chip type 'CytoScanHD_Array' (without requiring any
> tags) and with filename extension 'acs'.
>
>
> On Monday, December 15, 2014 6:27:51 PM UTC+2, Henrik Bengtsson wrote:
>>
>> I can reproduce this;
>>
>> > csv <- AffymetrixNetAffxCsvFile$byChipType(chipType)
>> Error in grep(pattern, basename(files0)) : invalid 'pattern' argument
>>
>> I'll investigate.
>>
>> /Henrik
>>
>> On Mon, Dec 15, 2014 at 5:51 AM, Chengyu Liu wrote:
>> > Hi,
>> >
>> > I am trying to read annotation file of CytoScanHD_Array, but somehow it
>> > could not locate it.
>> >
>> > I followed the tutorial in the web
>> > http://aroma-project.org/setup/annotationData/. I am using NetAffx
>> > Annotation Files (I could not find CDF file) .
>> > I created folder annotationData/chipTypes/CytoScanHD_Array/NetAffx/ and
>> > put
>> > annotation file CytoScanHD_Array_annot.csv there.
>> >
>> > I ran AffymetrixNetAffxCsvFile$byChipType("CytoScanHD_Array") at parent
>> > directory of annotationData.
>> >
>> > It gave error "Error in grep(pattern, basename(files0)) : invalid
>> > 'pattern'
>> > argument"
>> >
>> > Does anyone know what was wrong ?
>> &g
Re: [aroma.affymetrix] Could not loacate CystoScanHD_Array annotation
Try this instead:
csv <- AffymetrixNetAffxCsvFile$byChipType("CytoScanHD_Array",
pattern="_annot[.]csv")
I've updated http://aroma-project.org/setup/annotationData accordingly.
I'll try fix the bug forcing us to specifying 'pattern' this way.
Thanks for the report
/Henrik
On Mon, Dec 15, 2014 at 8:27 AM, Henrik Bengtsson wrote:
> I can reproduce this;
>
>> csv <- AffymetrixNetAffxCsvFile$byChipType(chipType)
> Error in grep(pattern, basename(files0)) : invalid 'pattern' argument
>
> I'll investigate.
>
> /Henrik
>
> On Mon, Dec 15, 2014 at 5:51 AM, Chengyu Liu wrote:
>> Hi,
>>
>> I am trying to read annotation file of CytoScanHD_Array, but somehow it
>> could not locate it.
>>
>> I followed the tutorial in the web
>> http://aroma-project.org/setup/annotationData/. I am using NetAffx
>> Annotation Files (I could not find CDF file) .
>> I created folder annotationData/chipTypes/CytoScanHD_Array/NetAffx/ and put
>> annotation file CytoScanHD_Array_annot.csv there.
>>
>> I ran AffymetrixNetAffxCsvFile$byChipType("CytoScanHD_Array") at parent
>> directory of annotationData.
>>
>> It gave error "Error in grep(pattern, basename(files0)) : invalid 'pattern'
>> argument"
>>
>> Does anyone know what was wrong ?
>>
>> Br,
>> C.Y
>>
>> --
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
>> version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to aroma-affymetrix@googlegroups.com
>> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>>
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to aroma-affymetrix+unsubscr...@googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
--
--
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version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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Re: [aroma.affymetrix] Could not loacate CystoScanHD_Array annotation
I can reproduce this;
> csv <- AffymetrixNetAffxCsvFile$byChipType(chipType)
Error in grep(pattern, basename(files0)) : invalid 'pattern' argument
I'll investigate.
/Henrik
On Mon, Dec 15, 2014 at 5:51 AM, Chengyu Liu wrote:
> Hi,
>
> I am trying to read annotation file of CytoScanHD_Array, but somehow it
> could not locate it.
>
> I followed the tutorial in the web
> http://aroma-project.org/setup/annotationData/. I am using NetAffx
> Annotation Files (I could not find CDF file) .
> I created folder annotationData/chipTypes/CytoScanHD_Array/NetAffx/ and put
> annotation file CytoScanHD_Array_annot.csv there.
>
> I ran AffymetrixNetAffxCsvFile$byChipType("CytoScanHD_Array") at parent
> directory of annotationData.
>
> It gave error "Error in grep(pattern, basename(files0)) : invalid 'pattern'
> argument"
>
> Does anyone know what was wrong ?
>
> Br,
> C.Y
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> ---
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to aroma-affymetrix+unsubscr...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
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Re: [aroma.affymetrix] Encountered ERROR while extracting chip effects
Hi,
you cannot use RMA on exon-arrays, you will need to use exon-aware
method such as FIRMA (e.g.
http://aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis).
Hope this helps
Henrik
PS. For http://aroma-project.org/replication/RMA, I've updated it to
use `theta <- extractTheta(ces)` instead of `theta <-
extractMatrix(ces)`. This will allow you to set the row names. But
as you'll find out, 'theta' becomes an JxKxI array for exon-arrays,
where J is the number of genes, I is the number of samples and K is
the maximum number of exons per gene found. In other words, using
doRMA() on exon arrays gives you at best exon-specific estimates (and
they are not very good estimates - FIRMA is doing a much better job on
that).
On Wed, Dec 10, 2014 at 1:51 AM, Rishi Das Roy wrote:
> Hi,
>
> I was trying to perform RMA on Mouse Exon 1.0 ST Array as described in aroma
> website (link) using custom cdf MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf.gz .
>
> I have executed following code in R
>
> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="coreR1,A20080718,MR")
> cs <- AffymetrixCelSet$byName("data_CEL", cdf=cdf);
> bc <- RmaBackgroundCorrection(cs);
> csB <- process(bc);
> qn <- QuantileNormalization(csB, typesToUpdate="pm");
> csN <- process(qn);
> plm <- RmaPlm(csN);
> fit(plm);
> ces <- getChipEffectSet(plm);
> theta <- extractMatrix(ces);
> rownames(theta) <- getUnitNames(cdf);
> Error in `rownames<-`(`*tmp*`, value = c("6838637", "6992377", "6901592", :
> length of 'dimnames' [1] not equal to array extent
>
> Please help me to understand this error and how can I solve this. The
> session info is given below.
>
> With regards
> Rishi
>
> R version 3.1.2 (2014-10-31)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=fi_FI.UTF-8LC_NUMERIC=CLC_TIME=en_GB
> LC_COLLATE=en_GBLC_MONETARY=fi_FI.UTF-8
> [6] LC_MESSAGES=en_GB LC_PAPER=en_GB LC_NAME=C
> LC_ADDRESS=CLC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GBLC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats4parallel stats graphics grDevices utils datasets
> methods base
>
> other attached packages:
> [1] preprocessCore_1.28.0 aroma.light_2.2.0
> aroma.affymetrix_2.12.8 aroma.core_2.12.8
> [5] R.devices_2.12.0 R.filesets_2.6.0
> R.utils_1.34.0R.oo_1.18.2
> [9] R.methodsS3_1.6.2 affxparser_1.38.0
> pd.moex10st.mm.aceviewg_0.0.1 affy_1.44.0
> [13] BiocInstaller_1.16.1 pd.moex.1.0.st.v1_3.10.0
> RSQLite_1.0.0 DBI_0.3.1
> [17] moex10stmmrefseqcdf_19.0.0AnnotationDbi_1.28.1
> GenomeInfoDb_1.2.3oligo_1.30.0
> [21] Biostrings_2.34.0 XVector_0.6.0
> IRanges_2.0.0 S4Vectors_0.4.0
> [25] Biobase_2.26.0oligoClasses_1.28.0
> BiocGenerics_0.12.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.34.0aroma.apd_0.5.0 base64enc_0.1-2
> bit_1.1-12 codetools_0.2-8 digest_0.6.5
> [7] DNAcopy_1.40.0 ff_2.2-13foreach_1.4.2
> GenomicRanges_1.18.3 iterators_1.0.7 matrixStats_0.12.2
> [13] PSCBS_0.43.0 R.cache_0.11.0 R.huge_0.8.0
> R.rsp_0.19.6 splines_3.1.2tools_3.1.2
> [19] zlibbioc_1.12.0
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> ---
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to aroma-affymetrix+unsubscr...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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Re: [aroma.affymetrix] using custom CDF file in aroma.affymetrix
I downloaded the two non-official CDFs
* HTA-2_0.r1.exon.cdf
* HTA-2_0.r1.gene.cdf
from
http://www.affymetrix.com/support/technical/byproduct.affx?product=human_transcriptome.
I then renamed them to use commas instead of periods for the "tags".
When I inspect them I see that they report an array dimension of
2572x2680 (=6892960), whereas your CDF reports 2560x2560 (=6553600).
The dimension of the CDF must much that of the CEL files. Are you
sure your CDF is correct? Where did you get yours from?
> cdf <- AffymetrixCdfFile$byChipType("HTA-2_0", tags="r1,exon")
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/HTA-2_0
Filename: HTA-2_0,r1,exon.cdf
File size: 818.80 MB (858574387 bytes)
Chip type: HTA-2_0,r1,exon
RAM: 0.00MB
File format: v3 (text; ASCII)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 914585
Cells per unit: 7.54
Number of QC units: 0
> cdf <- AffymetrixCdfFile$byChipType("HTA-2_0", tags="r1,gene")
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/HTA-2_0
Filename: HTA-2_0,r1,gene.cdf
File size: 467.96 MB (490696493 bytes)
Chip type: HTA-2_0,r1,gene
RAM: 0.00MB
File format: v3 (text; ASCII)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 70523
Cells per unit: 97.74
Number of QC units: 0
/Henrik
On Thu, Oct 16, 2014 at 8:54 AM, San wrote:
> Hi Henrik,
>
> Please see below:
>
>> sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] parallel stats graphics grDevices utils datasets methods
> base
>
> other attached packages:
> [1] preprocessCore_1.24.0 fdrtool_1.2.12 FIRMAGene_0.9.8
> aroma.light_1.32.0 matrixStats_0.10.0 aroma.affymetrix_2.12.0
> aroma.core_2.12.1 R.devices_2.11.0R.filesets_2.6.0
> gplots_2.14.2 limma_3.18.13 class_7.3-11
> [13] Biobase_2.22.0 BiocGenerics_0.8.0 R.utils_1.34.0
> R.oo_1.18.0 ggplot2_1.0.0 affxparser_1.34.2
> affy_1.40.0 R.methodsS3_1.6.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.30.0aroma.apd_0.5.0 base64enc_0.1-2
> BiocInstaller_1.12.1 bitops_1.0-6 caTools_1.17.1
> colorspace_1.2-4 digest_0.6.4 DNAcopy_1.36.0 gdata_2.13.3
> grid_3.0.2 gtable_0.1.2 gtools_3.4.1
> KernSmooth_2.23-13
> [15] MASS_7.3-35 munsell_0.4.2plyr_1.8.1
> proto_0.3-10 PSCBS_0.40.4 R.cache_0.10.0 R.huge_0.8.0
> R.rsp_0.19.0 Rcpp_0.11.3 reshape2_1.4 scales_0.2.4
> stringr_0.6.2tools_3.0.2 zlibbioc_1.8.0
>
>
>
> --
> View this message in context:
> http://aroma-affymetrix.967894.n3.nabble.com/aroma-affymetrix-using-custom-CDF-file-in-aroma-affymetrix-tp4025290p4025292.html
> Sent from the aroma.affymetrix mailing list archive at Nabble.com.
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
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Re: [aroma.affymetrix] using custom CDF file in aroma.affymetrix
This looks all correct to me. What is your sessionInfo() after
receiving this error?
/Henrik
On Wed, Oct 15, 2014 at 4:19 AM, sanjana wrote:
> Hi,
>
> I am using a Custom cdf file HTA-2_0,Transcript,binary.cdf in aroma.
> affymetrix to analyse HTA-2_0 chip . I am using the following commands to
> set up CDF and CEL files.
>
>>chipType <- "HTA-2_0"
>>cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Transcript,binary")
>>print(cdf)
>
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/HTA-2_0
> Filename: HTA-2_0,Transcript,binary.cdf
> File size: 7.55 MB (7921066 bytes)
> Chip type: HTA-2_0,Transcript,binary
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2560x2560
> Number of cells: 6553600
> Number of units: 18490
> Cells per unit: 354.44
> Number of QC units: 0
>
>>cs<-AffymetrixCelSet$byName("Krzy",cdf=cdf,verbose=verbose)
>
> However I am unable to read the CEL files as it gives me the following
> error:
>
> Error: Failed to setup a data set for any of 1 data directories located. The
> following reasons were reported: (1) Failed to create AffymetrixCdfFile
> object. Could not locate an annotation data file for chip type 'HTA-2_0'
> (without requiring any tags) and with filename extension 'cdf'. (while
> trying './rawData/Krzy/HTA-2_0').
>
> My directory structure is:
> annotationData< chipTypes rawData
> Please can someone help me understanding what I am doing wrong. I have used
> aroma.affymetrix for exon arrays and I never came across this issue. Is it
> something to do with the CDF file?
>
>
> Kind Regards,
> Sanjana
>
>
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
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> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> ---
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Re: [aroma.affymetrix] [process and display function in aroma.affymetrix]
On Sat, Sep 20, 2014 at 9:11 PM, jjspring OH wrote: > > > Thanks! Yes, it seems it is due to old version for manual example, > > > Everything is done when i follow the URL for now and getting display(ae) > result (attached file) > BTW just checking out for one warning message from plm fitting before > getting into alternative splicing part, > is it ok to ignore the message ? what exactly does it mean? > > > fit(plmTr, verbose=verbose) > > Warning message: > In fitfcn(y, ...) : > Ignoring a unit group when fitting probe-level model, because it has a > ridiculously large number of data points: 6515x8 > 5000x1 See 'models/RmaPlm/skipThreshold' on http://aroma-project.org/settings /Henrik >> > > > > > Thanks again, > Best Sunghee > > > > > > > 2014년 9월 21일 일요일 오전 1시 46분 6초 UTC+9, Henrik Bengtsson 님의 말: >> >> How are you setting up the ArrayExplorer? It looks like you're >> missing to set the color maps. Are you following a particular example >> (URL?) that could be wrong. Have a look at >> >> http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis >> >> for an example. >> >> /Henrik >> >> On Sat, Sep 20, 2014 at 4:03 AM, jjspring OH wrote: >> > >> > >> > And also, >> > >> > For process(ae) >> > >> > getting warning messages(pls see below) it seems to be related with next >> > command lines >> > it does not matter? could you please take a closer look at these as >> > well? >> > >> > curent sessionInfo is >> > >> > R version 3.1.1 (2014-07-10) >> > Platform: x86_64-apple-darwin10.8.0 (64-bit) >> > >> > locale: >> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> > >> > attached base packages: >> > [1] stats graphics grDevices utils datasets methods base >> > >> > other attached packages: >> > [1] R.rsp_0.19.3aroma.light_2.0.0 matrixStats_0.10.0 >> > [4] aroma.affymetrix_2.12.8 aroma.core_2.12.8 R.devices_2.11.4 >> > [7] R.filesets_2.6.0R.utils_1.33.7 R.oo_1.18.2 >> > [10] affxparser_1.36.0 R.methodsS3_1.6.1 >> > >> > loaded via a namespace (and not attached): >> > [1] aroma.apd_0.5.0 base64enc_0.1-2 digest_0.6.4DNAcopy_1.38.1 >> > [5] PSCBS_0.43.0R.cache_0.11.0 R.huge_0.8.0tools_3.1.1 >> >> >> > >> > >> > >> > >> > >> > >> > >> >> process(ae) >> > Loading required package: R.rsp >> > R.rsp v0.19.3 (2014-08-29) successfully loaded. See ?R.rsp for help. >> > >> > Attaching package: ‘R.rsp’ >> > >> > The following object is masked from ‘package:aroma.affymetrix’: >> > >> > getParameter >> > >> > The following objects are masked from ‘package:aroma.core’: >> > >> > getParameters, process, write >> > >> > The following objects are masked from ‘package:R.filesets’: >> > >> > getAttribute, getAttributes, getFile, getFileSize, getHeader, >> > nbrOfLines, setAttribute, setAttributes >> > >> > The following objects are masked from ‘package:R.utils’: >> > >> > parse, parse.default >> > >> > The following objects are masked from ‘package:base’: >> > >> > flush, parse, stop, write >> > >> > The following object is masked _by_ package:aroma.affymetrix: >> > >> > writeCdf >> > >> > The following object is masked _by_ package:R.utils: >> > >> > findFiles >> > >> > 20140920 19:48:32|Color maps: >> > 20140920 19:48:32|Chip type: RaGene-1_0-st-v1,r3 >> > 20140920 19:48:40|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _ >> > 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS >> > _ >> > 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS >> > _ >> > 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS >> > _ >> > 5_(RaGene-1_0-st-v1),residuals >> > 20140920 19:48:40|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _ >> > 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ >> > 8_(RaGene-1_0-st-v1), >> > NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _ >> > 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1) >> > 20140920 19:48:47|Col
Re: [aroma.affymetrix] [process and display function in aroma.affymetrix]
How are you setting up the ArrayExplorer? It looks like you're missing to set the color maps. Are you following a particular example (URL?) that could be wrong. Have a look at http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis for an example. /Henrik On Sat, Sep 20, 2014 at 4:03 AM, jjspring OH wrote: > > > And also, > > For process(ae) > > getting warning messages(pls see below) it seems to be related with next > command lines > it does not matter? could you please take a closer look at these as well? > > curent sessionInfo is > > R version 3.1.1 (2014-07-10) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] R.rsp_0.19.3aroma.light_2.0.0 matrixStats_0.10.0 > [4] aroma.affymetrix_2.12.8 aroma.core_2.12.8 R.devices_2.11.4 > [7] R.filesets_2.6.0R.utils_1.33.7 R.oo_1.18.2 > [10] affxparser_1.36.0 R.methodsS3_1.6.1 > > loaded via a namespace (and not attached): > [1] aroma.apd_0.5.0 base64enc_0.1-2 digest_0.6.4DNAcopy_1.38.1 > [5] PSCBS_0.43.0R.cache_0.11.0 R.huge_0.8.0tools_3.1.1 >> > > > > > > > >> process(ae) > Loading required package: R.rsp > R.rsp v0.19.3 (2014-08-29) successfully loaded. See ?R.rsp for help. > > Attaching package: ‘R.rsp’ > > The following object is masked from ‘package:aroma.affymetrix’: > > getParameter > > The following objects are masked from ‘package:aroma.core’: > > getParameters, process, write > > The following objects are masked from ‘package:R.filesets’: > > getAttribute, getAttributes, getFile, getFileSize, getHeader, > nbrOfLines, setAttribute, setAttributes > > The following objects are masked from ‘package:R.utils’: > > parse, parse.default > > The following objects are masked from ‘package:base’: > > flush, parse, stop, write > > The following object is masked _by_ package:aroma.affymetrix: > > writeCdf > > The following object is masked _by_ package:R.utils: > > findFiles > > 20140920 19:48:32|Color maps: > 20140920 19:48:32|Chip type: RaGene-1_0-st-v1,r3 > 20140920 19:48:40|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _ > 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS _ > 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS _ > 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS _ > 5_(RaGene-1_0-st-v1),residuals > 20140920 19:48:40|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _ > 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ 8_(RaGene-1_0-st-v1), > NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _ > 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1) > 20140920 19:48:47|Color maps: > 20140920 19:48:47|Chip type: RaGene-1_0-st-v1,r3 > 20140920 19:48:54|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _ > 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS _ > 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS _ > 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS _ > 5_(RaGene-1_0-st-v1),residuals > 20140920 19:48:54|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _ > 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ 8_(RaGene-1_0-st-v1), > NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _ > 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1) > [1] FALSE > Warning messages: > 1: In fcn(...) : Packages reordered in search path: package:affxparser > 2: In parseRepos(sets = repos, where = where, fallback = fallback, : > Had to fall back to a set of predefined repositories (please make sure to > set your package repositories properly, cf. ?setRepositories): CRAN: > ‘@CRAN@’ -> ‘http://cran.r-project.org’ > 3: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' > 4: In writeImages.SpatialReporter(reporter, arrays = arrays, aliases = > aliases, : > No color maps specified. Nothing to do. > 5: In parseRepos(sets = repos, where = where, fallback = fallback, : > Had to fall back to a set of predefined repositories (please make sure to > set your package repositories properly, cf. ?setRepositories): CRAN: > ‘@CRAN@’ -> ‘http://cran.r-project.org’ > 6: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' > > > > > Many Thanks! > > Sunghee > > > 2014년 9월 20일 토요일 오후 7시 58분 39초 UTC+9, jjspring OH 님의 말: >> >> >> >> >> Thanks Henrik, >> >> Ye
Re: [aroma.affymetrix] [process and display function in aroma.affymetrix]
On Fri, Sep 19, 2014 at 8:24 AM, Henrik Bengtsson wrote:
> Sorry, it took me a while to spot the actual problem;
>
>> display(ae)
>> The file
>> /foo/arom-anal/\foo\arom-anal\reports\tissues\RBC,QN,RMA\ArrayExplorer.html
>> does not exist.
>
> (I'm surprised there is no "error" or similar generated, but it could
> be because that message is from an external software).
>
> You can always open the HTML report manually just like any other HTML
> file. You'll find it at reports\tissues/RBC,QN,RMA/ArrayExplorer.html
> under your working directory.
>
> I'll investigate and fix this.
It was a bug in aroma.core making display() only opening Explorer HTML
pages on Windows. I've fixed this in aroma.core 2.12.8 and verified
that it works on OSX. Update to via:
source("http://callr.org/install#aroma.affymetrix";)
Thanks for reporting
Henrik
>
> /Henrik
>
>
>
> On Wed, Sep 17, 2014 at 5:50 PM, jjspring OH wrote:
>>
>> Hi,
>>
>>
>> I am getting errors when i run aroma.affymetrix package for dynamic reports,
>> it looks like for low level analysis, everything works well for now,
>> Could you please take a closer look at and let me know what the problem is?
>> I am running under the current directory(/foo/arom-anal/)
>>
>>
>>> process(ae)
>> Loading required package: R.rsp
>> R.rsp v0.19.3 (2014-08-29) successfully loaded. See ?R.rsp for help.
>>
>> Attaching package: ‘R.rsp’
>>
>> The following object is masked from ‘package:aroma.affymetrix’:
>>
>> getParameter
>>
>> The following objects are masked from ‘package:aroma.core’:
>>
>> getParameters, process, write
>>
>> The following objects are masked from ‘package:R.filesets’:
>>
>> getAttribute, getAttributes, getFile, getFileSize, getHeader,
>> nbrOfLines, setAttribute, setAttributes
>>
>> The following objects are masked from ‘package:R.utils’:
>>
>> parse, parse.default
>>
>> The following objects are masked from ‘package:base’:
>>
>> flush, parse, stop, write
>>
>> The following object is masked _by_ package:aroma.affymetrix:
>>
>> writeCdf
>>
>> The following object is masked _by_ package:R.utils:
>>
>> findFiles
>>
>> 20140918 09:43:05|Color maps:
>> 20140918 09:43:05|Chip type: RaGene-1_0-st-v1,r3
>> 20140918 09:43:12|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _
>> 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS _
>> 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS _
>> 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS _
>> 5_(RaGene-1_0-st-v1),residuals
>> 20140918 09:43:12|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _
>> 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ 8_(RaGene-1_0-st-v1),
>> NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _
>> 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1)
>> 20140918 09:43:20|Color maps:
>> 20140918 09:43:20|Chip type: RaGene-1_0-st-v1,r3
>> 20140918 09:43:27|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _
>> 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS _
>> 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS _
>> 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS _
>> 5_(RaGene-1_0-st-v1),residuals
>> 20140918 09:43:27|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _
>> 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ 8_(RaGene-1_0-st-v1),
>> NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _
>> 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1)
>> [1] FALSE
>> Warning messages:
>> 1: In fcn(...) : Packages reordered in search path: package:affxparser
>> 2: In parseRepos(sets = repos, where = where, fallback = fallback, :
>> Had to fall back to a set of predefined repositories (please make sure to
>> set your package repositories properly, cf. ?setRepositories): CRAN:
>> ‘@CRAN@’ -> ‘http://cran.r-project.org’
>> 3: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
>> 4: In writeImages.SpatialReporter(reporter, arrays = arrays, aliases =
>> aliases, :
>> No color maps specified. Nothing to do.
>> 5: In parseRepos(sets = repos, where = where, fallback = fallback, :
>> Had to fall back to a set of predefined repositories (please make sure to
>> set your package repositories properly, cf. ?setRepositories): CRAN:
>> ‘@CRAN@’ -> ‘http://cran.r-project.org’
>> 6: In is.na(
Re: [aroma.affymetrix] [process and display function in aroma.affymetrix]
Sorry, it took me a while to spot the actual problem; > display(ae) > The file > /foo/arom-anal/\foo\arom-anal\reports\tissues\RBC,QN,RMA\ArrayExplorer.html > does not exist. (I'm surprised there is no "error" or similar generated, but it could be because that message is from an external software). You can always open the HTML report manually just like any other HTML file. You'll find it at reports\tissues/RBC,QN,RMA/ArrayExplorer.html under your working directory. I'll investigate and fix this. /Henrik On Wed, Sep 17, 2014 at 5:50 PM, jjspring OH wrote: > > Hi, > > > I am getting errors when i run aroma.affymetrix package for dynamic reports, > it looks like for low level analysis, everything works well for now, > Could you please take a closer look at and let me know what the problem is? > I am running under the current directory(/foo/arom-anal/) > > >> process(ae) > Loading required package: R.rsp > R.rsp v0.19.3 (2014-08-29) successfully loaded. See ?R.rsp for help. > > Attaching package: ‘R.rsp’ > > The following object is masked from ‘package:aroma.affymetrix’: > > getParameter > > The following objects are masked from ‘package:aroma.core’: > > getParameters, process, write > > The following objects are masked from ‘package:R.filesets’: > > getAttribute, getAttributes, getFile, getFileSize, getHeader, > nbrOfLines, setAttribute, setAttributes > > The following objects are masked from ‘package:R.utils’: > > parse, parse.default > > The following objects are masked from ‘package:base’: > > flush, parse, stop, write > > The following object is masked _by_ package:aroma.affymetrix: > > writeCdf > > The following object is masked _by_ package:R.utils: > > findFiles > > 20140918 09:43:05|Color maps: > 20140918 09:43:05|Chip type: RaGene-1_0-st-v1,r3 > 20140918 09:43:12|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _ > 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS _ > 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS _ > 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS _ > 5_(RaGene-1_0-st-v1),residuals > 20140918 09:43:12|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _ > 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ 8_(RaGene-1_0-st-v1), > NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _ > 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1) > 20140918 09:43:20|Color maps: > 20140918 09:43:20|Chip type: RaGene-1_0-st-v1,r3 > 20140918 09:43:27|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _ > 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS _ > 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS _ > 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS _ > 5_(RaGene-1_0-st-v1),residuals > 20140918 09:43:27|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _ > 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ 8_(RaGene-1_0-st-v1), > NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _ > 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1) > [1] FALSE > Warning messages: > 1: In fcn(...) : Packages reordered in search path: package:affxparser > 2: In parseRepos(sets = repos, where = where, fallback = fallback, : > Had to fall back to a set of predefined repositories (please make sure to > set your package repositories properly, cf. ?setRepositories): CRAN: > ‘@CRAN@’ -> ‘http://cran.r-project.org’ > 3: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' > 4: In writeImages.SpatialReporter(reporter, arrays = arrays, aliases = > aliases, : > No color maps specified. Nothing to do. > 5: In parseRepos(sets = repos, where = where, fallback = fallback, : > Had to fall back to a set of predefined repositories (please make sure to > set your package repositories properly, cf. ?setRepositories): CRAN: > ‘@CRAN@’ -> ‘http://cran.r-project.org’ > 6: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' >> display(ae) >> The file >> /foo/arom-anal/\foo\arom-anal\reports\tissues\RBC,QN,RMA\ArrayExplorer.html >> does not exist. > > > Thanks a lot in advance, > > Sunghee > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- When re
Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)
I've narrowed down this bug to the R.utils package and fixed it. I've
verified that the RMA pipeline now also works running in /tmp/.
Update aroma.affymetrix (including R.utils) by running:
source("http://callr.org/install#aroma.affymetrix";)
in a fresh R session.
/Henrik
On Tue, Sep 16, 2014 at 11:11 PM, jjspring OH wrote:
> Finally working well after changing into one step further deeper directory
> as your comment,
>
> Sunghee
>
>
> 2014년 9월 17일 수요일 오후 3시 2분 20초 UTC+9, Henrik Bengtsson 님의 말:
>>
>> (Back to the public forum)
>>
>> REPRODUCIBLE EXAMPLE:
>> It's a bug (still to be found) that shows itself when one runs the
>> analysis in one directory up from the root /, e.g. /arom-anal/. I
>> managed to reproduce this by running a standard analysis in /tmp/.
>>
>> WORKAROUND:
>> Run the analysis in directory that is at least one step deeper, e.g.
>> /foo/arom-anal/. The problem goes away when I run the analysis in
>> /tmp/foo/.
>>
>> Please confirm that the above workaround also works for you and thanks
>> for reporting on this. I'll fix the bug as soon as I can.
>>
>> /Henrik
>>
>> On Tue, Sep 16, 2014 at 10:52 PM, jjspring OH wrote:
>> >
>> >
>> > yes it is working
>> >
>> >>
>> >> Arguments$getReadablePath("plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1")
>> > [1] "plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1"
>> >
>> >
>> > Sunghee
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > Sunghee Oh, PhD
>> > Director, Kim Sook Za Children's Hospital Medical Center Research
>> > Foundation,
>> > 745 JikJi Daero Heung Deok Gu
>> > Cheng Ju City Chung Buk
>> > 361-841, S. Korea
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > On Wed, Sep 17, 2014 at 2:48 PM, Henrik Bengtsson
>> >
>> > wrote:
>> >>
>> >> Let's continue this off the list to spare the others the noise and
>> >> post back when we found the solution.
>> >>
>> >> Continuing, and before I'll have to dig into the low-level code to
>> >> figure out why you possibly could get this weird problem, does
>> >>
>> >>
>> >> Arguments$getReadablePath("plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1")
>> >>
>> >> work as well?
>> >>
>> >> /Henrik
>> >>
>> >>
>> >>
>> >> On Tue, Sep 16, 2014 at 10:40 PM, jjspring OH
>> >> wrote:
>> >> >
>> >> >
>> >> >
>> >> > Hi Henrik,
>> >> >
>> >> > See the outputs:
>> >> >
>> >> >> path <- getPath(plm)
>> >> >> print(path)
>> >> > [1] "plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1"
>> >> >> dir("plmData")
>> >> > [1] "tissues,RBC,QN,RMA""tissues,RBC,QN,RMA,merged"
>> >> >> isDirectory("plmData")
>> >> > [1] TRUE
>> >> >> Arguments$getReadablePath("plmData")
>> >> > [1] "plmData"
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > 2014년 9월 17일 수요일 오후 2시 14분 45초 UTC+9, Henrik Bengtsson 님의 말:
>> >> >>
>> >> >> Ok, and then the output of:
>> >> >>
>> >> >> path <- getPath(plm)
>> >> >> print(path)
>> >> >> dir("plmData")
>> >> >> isDirectory("plmData")
>> >> >> Arguments$getReadablePath("plmData")
>> >> >>
>> >> >> /H
>> >> >>
>> >> >>
>> >> >> On Tue, Sep 16, 2014 at 9:57 PM, jjspring OH
>> >> >> wrote:
>> >> >> > Hi Henrik,
>> >> >> >
>> >> >> > See below:
>> >> >> >
>> >> >> >
>> >> >> >> print(plm)
>> >> >> > RmaPlm:
>> >> >
Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)
(Back to the public forum)
REPRODUCIBLE EXAMPLE:
It's a bug (still to be found) that shows itself when one runs the
analysis in one directory up from the root /, e.g. /arom-anal/. I
managed to reproduce this by running a standard analysis in /tmp/.
WORKAROUND:
Run the analysis in directory that is at least one step deeper, e.g.
/foo/arom-anal/. The problem goes away when I run the analysis in
/tmp/foo/.
Please confirm that the above workaround also works for you and thanks
for reporting on this. I'll fix the bug as soon as I can.
/Henrik
On Tue, Sep 16, 2014 at 10:52 PM, jjspring OH wrote:
>
>
> yes it is working
>
>> Arguments$getReadablePath("plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1")
> [1] "plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1"
>
>
> Sunghee
>
>
>
>
>
>
>
>
>
>
>
> Sunghee Oh, PhD
> Director, Kim Sook Za Children's Hospital Medical Center Research
> Foundation,
> 745 JikJi Daero Heung Deok Gu
> Cheng Ju City Chung Buk
> 361-841, S. Korea
>
>
>
>
>
>
>
>
> On Wed, Sep 17, 2014 at 2:48 PM, Henrik Bengtsson
> wrote:
>>
>> Let's continue this off the list to spare the others the noise and
>> post back when we found the solution.
>>
>> Continuing, and before I'll have to dig into the low-level code to
>> figure out why you possibly could get this weird problem, does
>>
>> Arguments$getReadablePath("plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1")
>>
>> work as well?
>>
>> /Henrik
>>
>>
>>
>> On Tue, Sep 16, 2014 at 10:40 PM, jjspring OH
>> wrote:
>> >
>> >
>> >
>> > Hi Henrik,
>> >
>> > See the outputs:
>> >
>> >> path <- getPath(plm)
>> >> print(path)
>> > [1] "plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1"
>> >> dir("plmData")
>> > [1] "tissues,RBC,QN,RMA""tissues,RBC,QN,RMA,merged"
>> >> isDirectory("plmData")
>> > [1] TRUE
>> >> Arguments$getReadablePath("plmData")
>> > [1] "plmData"
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > 2014년 9월 17일 수요일 오후 2시 14분 45초 UTC+9, Henrik Bengtsson 님의 말:
>> >>
>> >> Ok, and then the output of:
>> >>
>> >> path <- getPath(plm)
>> >> print(path)
>> >> dir("plmData")
>> >> isDirectory("plmData")
>> >> Arguments$getReadablePath("plmData")
>> >>
>> >> /H
>> >>
>> >>
>> >> On Tue, Sep 16, 2014 at 9:57 PM, jjspring OH
>> >> wrote:
>> >> > Hi Henrik,
>> >> >
>> >> > See below:
>> >> >
>> >> >
>> >> >> print(plm)
>> >> > RmaPlm:
>> >> > Data set: tissues
>> >> > Chip type: RaGene-1_0-st-v1,r3
>> >> > Input tags: RBC,QN
>> >> > Output tags: RBC,QN,RMA
>> >> > Parameters: {probeModel: chr "pm", shift: num 0, flavor: chr
>> >> > "affyPLM",
>> >> > treatNAsAs: chr "weights"}
>> >> > Path: plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1
>> >> > RAM: 0.00MB
>> >> >> print(getwd())
>> >> > [1] "/arom-anal"
>> >> >
>> >> >
>> >> > Thanks
>> >> > Sunghee
>> >> >
>> >> >
>> >> > 2014년 9월 17일 수요일 오후 1시 45분 53초 UTC+9, Henrik Bengtsson 님의 말:
>> >> >>
>> >> >> That is really odd and I've never seen that error (8-9 years now).
>> >> >> There must be a simple answer to this. What does:
>> >> >>
>> >> >> print(plm)
>> >> >> print(getwd())
>> >> >>
>> >> >> output when you get to that step.
>> >> >>
>> >> >> /Henrik
>> >> >>
>> >> >>
>> >> >> On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH
>> >> >> wrote:
>> >> >> >
>> >> >> >
>> >> >> > Hi,
>> >> >> >
>> >> >> > After setting up the directory, performed background correction
>> >> >> > and
>> >>
Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)
Ok, and then the output of:
path <- getPath(plm)
print(path)
dir("plmData")
isDirectory("plmData")
Arguments$getReadablePath("plmData")
/H
On Tue, Sep 16, 2014 at 9:57 PM, jjspring OH wrote:
> Hi Henrik,
>
> See below:
>
>
>> print(plm)
> RmaPlm:
> Data set: tissues
> Chip type: RaGene-1_0-st-v1,r3
> Input tags: RBC,QN
> Output tags: RBC,QN,RMA
> Parameters: {probeModel: chr "pm", shift: num 0, flavor: chr "affyPLM",
> treatNAsAs: chr "weights"}
> Path: plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1
> RAM: 0.00MB
>> print(getwd())
> [1] "/arom-anal"
>
>
> Thanks
> Sunghee
>
>
> 2014년 9월 17일 수요일 오후 1시 45분 53초 UTC+9, Henrik Bengtsson 님의 말:
>>
>> That is really odd and I've never seen that error (8-9 years now).
>> There must be a simple answer to this. What does:
>>
>> print(plm)
>> print(getwd())
>>
>> output when you get to that step.
>>
>> /Henrik
>>
>>
>> On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH wrote:
>> >
>> >
>> > Hi,
>> >
>> > After setting up the directory, performed background correction and rank
>> > based quantile normalization,
>> >
>> >
>> >
>> > library(aroma.affymetrix)
>> >
>> > verbose <- Arguments$getVerbose(-8, timestamp=T)
>> >
>> > chipType <- "RaGene-1_0-st-v1"
>> >
>> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3")
>> >
>> > cs <- AffymetrixCelSet$byName("tissues",cdf=cdf)
>> >
>> >
>> > print(cs)
>> >
>> >
>> >> cs
>> > AffymetrixCelSet:
>> > Name: tissues
>> > Tags:
>> > Path: ../../arom-anal/rawData/tissues/RaGene-1_0-st-v1
>> > Platform: Affymetrix
>> > Chip type: RaGene-1_0-st-v1,r3
>> > Number of arrays: 8
>> > Names: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1), CS _
>> > 7_(RaGene-1_0-st-v1), ..., NS _ 5_(RaGene-1_0-st-v1) [8]
>> > Time period: 2012-06-02 14:22:20 -- 2012-06-02 16:29:33
>> > Total file size: 84.50MB
>> > RAM: 0.01MB
>> >
>> >
>> > bc <- RmaBackgroundCorrection(cs)
>> >
>> > csBC <- process(bc,verbose=verbose)
>> >
>> >
>> >
>> > qn <- QuantileNormalization(csBC, typesToUpdate = "pm")
>> >
>> > print(qn)
>> >
>> > csN <- process(qn, verbose = verbose)
>> >
>> > plm <- RmaPlm(csN)
>> >
>> > print(plm)
>> >
>> >
>> >
>> > Until here, looks fine, BUT, when i perform fit function as below and
>> > the
>> > errors come out related with directory,
>> >
>> > fit(plm, verbose = verbose)
>> >
>> > qam <- QualityAssessmentModel(plm)
>> >
>> > #plotNuse(qam)
>> >
>> > plotRle(qam)
>> >
>> >
>> >
>> > current directory is /arom-anal, and setting up the data files
>> > (annotation,
>> > cel files, and raw data) look fine(see below hierarchical structure of
>> > directories),
>> > After you take a closer look at the following errors, could you please
>> > let
>> > me know what the problems are?
>> >
>> >
>> >
>> > Creating CEL file...done
>> > [2014-09-17 13:29:59] Exception: Pathname not found:
>> >
>> > arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/probeAffinities.CEL
>> > (none of the parent directories
>> > [arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/] exist; current
>> > directory is '/arom-anal')
>> >
>> > at #22. getReadablePathname.Arguments(static, ...)
>> > - getReadablePathname.Arguments() is in environment 'R.utils'
>> >
>> > at #21. getReadablePathname(static, ...)
>> > - getReadablePathname() is in environment 'R.utils'
>> > - originating from ''
>> >
>> > at #20. Arguments$getReadablePathname(filename, path = path,
>> > absolutePath
>> > = TRUE,
>> > mustExist = mustExist)
>> > - Arguments$getReadablePathname() is local of the calling
>> > function
>> >
>> > at #19. GenericDataFile(...)
>> > - GenericDataFile() is in environment 'R.filesets'
>> >
>>
Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)
That is really odd and I've never seen that error (8-9 years now).
There must be a simple answer to this. What does:
print(plm)
print(getwd())
output when you get to that step.
/Henrik
On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH wrote:
>
>
> Hi,
>
> After setting up the directory, performed background correction and rank
> based quantile normalization,
>
>
>
> library(aroma.affymetrix)
>
> verbose <- Arguments$getVerbose(-8, timestamp=T)
>
> chipType <- "RaGene-1_0-st-v1"
>
> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3")
>
> cs <- AffymetrixCelSet$byName("tissues",cdf=cdf)
>
>
> print(cs)
>
>
>> cs
> AffymetrixCelSet:
> Name: tissues
> Tags:
> Path: ../../arom-anal/rawData/tissues/RaGene-1_0-st-v1
> Platform: Affymetrix
> Chip type: RaGene-1_0-st-v1,r3
> Number of arrays: 8
> Names: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1), CS _
> 7_(RaGene-1_0-st-v1), ..., NS _ 5_(RaGene-1_0-st-v1) [8]
> Time period: 2012-06-02 14:22:20 -- 2012-06-02 16:29:33
> Total file size: 84.50MB
> RAM: 0.01MB
>
>
> bc <- RmaBackgroundCorrection(cs)
>
> csBC <- process(bc,verbose=verbose)
>
>
>
> qn <- QuantileNormalization(csBC, typesToUpdate = "pm")
>
> print(qn)
>
> csN <- process(qn, verbose = verbose)
>
> plm <- RmaPlm(csN)
>
> print(plm)
>
>
>
> Until here, looks fine, BUT, when i perform fit function as below and the
> errors come out related with directory,
>
> fit(plm, verbose = verbose)
>
> qam <- QualityAssessmentModel(plm)
>
> #plotNuse(qam)
>
> plotRle(qam)
>
>
>
> current directory is /arom-anal, and setting up the data files (annotation,
> cel files, and raw data) look fine(see below hierarchical structure of
> directories),
> After you take a closer look at the following errors, could you please let
> me know what the problems are?
>
>
>
> Creating CEL file...done
> [2014-09-17 13:29:59] Exception: Pathname not found:
> arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/probeAffinities.CEL
> (none of the parent directories
> [arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/] exist; current
> directory is '/arom-anal')
>
> at #22. getReadablePathname.Arguments(static, ...)
> - getReadablePathname.Arguments() is in environment 'R.utils'
>
> at #21. getReadablePathname(static, ...)
> - getReadablePathname() is in environment 'R.utils'
> - originating from ''
>
> at #20. Arguments$getReadablePathname(filename, path = path, absolutePath
> = TRUE,
> mustExist = mustExist)
> - Arguments$getReadablePathname() is local of the calling function
>
> at #19. GenericDataFile(...)
> - GenericDataFile() is in environment 'R.filesets'
>
> at #18. extend(GenericDataFile(...), c("AromaMicroarrayDataFile",
> uses("FileCacheKeyInterface")))
> - extend() is in environment 'R.oo'
>
> at #17. AromaMicroarrayDataFile(...)
> - AromaMicroarrayDataFile() is in environment 'aroma.core'
>
> at #16. extend(AromaMicroarrayDataFile(...), c("AffymetrixFile",
> uses("AromaPlatformInterface")))
> - extend() is in environment 'R.oo'
>
> at #15. AffymetrixFile(...)
> - AffymetrixFile() is in environment 'aroma.affymetrix'
>
> at #14. extend(AffymetrixFile(...), "AffymetrixCelFile", `cached:.header`
> = NULL,
> `cached:.lastPlotData` = NULL, .cdf = NULL)
> - extend() is in environment 'R.oo'
>
> at #13. AffymetrixCelFile(...)
> - AffymetrixCelFile() is in environment 'aroma.affymetrix'
>
> at #12. extend(AffymetrixCelFile(...), c("ParameterCelFile",
> uses("ParametersInterface")),
> `cached:.readUnitsCache` = NULL, encodeFunction =
> encodeFunction,
> decodeFunction = decodeFunction)
> - extend() is in environment 'R.oo'
>
> at #11. ParameterCelFile(...)
> - ParameterCelFile() is in environment 'aroma.affymetrix'
>
> at #10. extend(ParameterCelFile(...), "ProbeAffinityFile",
> `cached:.firstCells` = NULL,
> probeModel = probeModel)
> - extend() is in environment 'R.oo'
>
> at #09. this(...)
> - this() is in environment 'aroma.affymetrix'
>
> at #08. newInstance.Class(.class, getPathname(paf), cdf = getCdf(ds),
> probeModel = this$probeModel)
> - newInstance.Class() is in environment 'R.oo'
>
> at #07. newInstance(.class, getPathname(paf), cdf = getCdf(ds), probeModel
> = this$probeModel)
> - newInstance() is in environment 'R.oo'
>
> at #06. getProbeAffinityFile.ProbeLevelModel(this, verbose =
> less(verbose))
> - getProbeAffinityFile.ProbeLevelModel() is in environment
> 'aroma.affymetrix'
>
> at #05. NextMethod("getProbeAffinityFile")
> - NextMethod() is in environment 'base'
>
> at #04. getProbeAffinityFile.RmaPlm(this, verbose = less(verbose))
> - getProbeAffinityFile.RmaPlm() is in environment
> 'aroma.affymetrix'
>
> at #03. getProbeAffinityFile(this, verbose = less(verbose))
> -
Re: [aroma.affymetrix] Errors on setup working directory
Note that there should be/is a comma after the chip type prefix 'RaGene-1_0-st-v1', so rename that 'RaGene-1_0-st-v1.r3.cdf' to 'RaGene-1_0-st-v1,r3.cdf' and retry. You find some information on this in http://aroma-project.org/setup/annotationData and illustrated in http://aroma-project.org/vignettes/GeneSTArrayAnalysis Hope this helps Henrik On Sun, Sep 14, 2014 at 10:11 PM, jjspring OH wrote: > Hi > > I am working on aroma.affymetrix package, > btw, it seems like i set up the annotationDat and rawData directory under > the current working directory(/arom-anal) right, > but not working when i upload cdf file with cdf <- > AffymetrixCdfFile$byChipType(chipType, tags="r3") > > Please see my sessionInfo() in R and also, directory information as below: > > Plus, in order to easily describe the case, i have attached working > directory image files in which annotation and cel files exist as well, > > Please let me know if there is something wrong, > > > = >>> > > > > > In R, > > > >> verbose <- Arguments$getVerbose(-8, timestamp=T) > >> chipType <- "RaGene-1_0-st-v1" > >> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3") > > [2014-09-15 14:03:25] Exception: Failed to create AffymetrixCdfFile object. > Could not locate an annotation data file for chip type 'RaGene-1_0-st-v1' > with tags 'r3' and with filename extension 'cdf'. > > > at #03. byChipType.UnitAnnotationDataFile(static, ...) > > - byChipType.UnitAnnotationDataFile() is in environment > 'aroma.core' > > > at #02. byChipType(static, ...) > > - byChipType() is in environment 'aroma.core' > > - originating from '' > > > at #01. AffymetrixCdfFile$byChipType(chipType, tags = "r3") > > - AffymetrixCdfFile$byChipType() is local of the calling function > > > Error: Failed to create AffymetrixCdfFile object. Could not locate an > annotation data file for chip type 'RaGene-1_0-st-v1' with tags 'r3' and > with filename extension 'cdf'. > >> > > > > > > > > >> help(AffymetrixCdfFile) > >> getwd() > > [1] "/arom-anal" > >> quit() > > Save workspace image? [y/n/c]: n > > verdas-MacBook-Pro:arom-anal sungheeoh$ ls > > annotationData rawData > > verdas-MacBook-Pro:arom-anal sungheeoh$ cd annotationData/ > > verdas-MacBook-Pro:annotationData sungheeoh$ cd .. > > verdas-MacBook-Pro:arom-anal sungheeoh$ cd rawData/ > > verdas-MacBook-Pro:rawData sungheeoh$ ls > > tissues > > verdas-MacBook-Pro:rawData sungheeoh$ cd tissues > > verdas-MacBook-Pro:tissues sungheeoh$ ls > > RaGene-1_0-st-v1 > > verdas-MacBook-Pro:tissues sungheeoh$ cd RaGene-1_0-st-v1/ > > verdas-MacBook-Pro:RaGene-1_0-st-v1 sungheeoh$ ls > > CS _ 10_(RaGene-1_0-st-v1).CEL CS _ 7_(RaGene-1_0-st-v1).CEL NS _ > 1_(RaGene-1_0-st-v1).CEL NS _ 4_(RaGene-1_0-st-v1).CEL > > CS _ 12_(RaGene-1_0-st-v1).CEL CS _ 8_(RaGene-1_0-st-v1).CEL NS _ > 3_(RaGene-1_0-st-v1).CEL NS _ 5_(RaGene-1_0-st-v1).CEL > > verdas-MacBook-Pro:RaGene-1_0-st-v1 sungheeoh$ cd .. > > verdas-MacBook-Pro:tissues sungheeoh$ cd .. > > verdas-MacBook-Pro:rawData sungheeoh$ cd .. > > verdas-MacBook-Pro:arom-anal sungheeoh$ cd annotationData/ > > verdas-MacBook-Pro:annotationData sungheeoh$ ls > > chipTypes > > verdas-MacBook-Pro:annotationData sungheeoh$ cd chipTypes/ > > verdas-MacBook-Pro:chipTypes sungheeoh$ ls > > RaGene-1_0-st-v1 > > verdas-MacBook-Pro:chipTypes sungheeoh$ cd RaGene-1_0-st-v1/ > > verdas-MacBook-Pro:RaGene-1_0-st-v1 sungheeoh$ ls > > RaGene-1_0-st-v1.r3.cdf > > verdas-MacBook-Pro:RaGene-1_0-st-v1 sungheeoh$ R > > > > > R version 3.1.1 (2014-07-10) > > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > > locale: > > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > Thanks, Sunghee > > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post
Re: [aroma.affymetrix] Error when analyzing CEL files using process() function: "No permission to modify existing file: /probeData..."
I've updated aroma.affymetrix v2.11.8 and friends. Update by:
source("http://callr.org/install#aroma.affymetrix";)
I'd be keen to hear whether this solves your problem or not.
/Henrik
On Thu, Sep 4, 2014 at 1:47 PM, Henrik Bengtsson wrote:
> Hi,
>
> good that it works for you with this workaround. The fix in aroma is
> fairly simple(*). I'll let you know when an updated version is
> available.
>
> (*) DETAILS: This has to do with base::file.copy() and its argument
> 'copy.mode' which was introduced in R 2.13.0 (April 2011). The thing
> is that they set the default to TRUE (whereas the previous behavior
> was equivalent to FALSE), meaning any files copied will inherit the
> file permissions from the source. Various steps in the aroma pipeline
> *copies* the source CEL file and uses that as a template to store
> updates signals. This is what hits you. I'll updating to make use of
> base::file.copy(..., copy.mode=FALSE) such that one can work with also
> read-only CEL files.
>
> Thanks for reporting on this (not too unlikely) use case
>
> Henrik
>
> On Thu, Sep 4, 2014 at 1:35 PM, Taylor Raborn wrote:
>> Hi Henrik:
>>
>> Thank you for the prompt reply. You are right- the .CEL files are all read
>> only (see their permissions, below)
>>
>> rtraborn@Mason:
>> /N/dc2/scratch/rtraborn/ML_Project/NIK_2014/rawData/NIK_2014/HuEx-1_0-st-v2>
>> ls -lkhtra
>>
>>
>> -r--r--r-- 1 ... 63M Jan 25 2011 GSM709338_HSB194-VFC-R.CEL
>>
>> -r--r--r-- 1 ... 63M Jan 25 2011 GSM709337_HSB194-VFC-L.CEL
>>
>> -r--r--r-- 1 ... 63M Jan 25 2011 GSM709336_HSB194-V1C-R.CEL
>>
>> -r--r--r-- 1 ... 63M Jan 25 2011 GSM709335_HSB194-V1C-L.CEL
>>
>> -r--r--r-- 1 ... 63M Jan 25 2011 GSM709334_HSB194-STR-L.CEL
>>
>> -r--r--r-- 1 ... 63M Jan 25 2011 GSM709333_HSB194-STC-R.CEL
>>
>> -r--r--r-- 1 ... 63M Jan 25 2011 GSM709332_HSB194-STC-L.CEL
>>
>> -r--r--r-- 1 ... 63M Jan 25 2011 GSM709331_HSB194-S1C-R.CEL
>>
>> -r--r--r-- 1 ... 63M Jan 25 2011 GSM709330_HSB194-S1C-L.CEL
>>
>>
>> After changing the permissions, the job performed without issue (I'm showing
>> you only the results of 1/9 for the sake of brevity):
>>
>>> csBC <- process(bc,verbose=verbose)
>>
>> Background correcting data set...
>>
>> Number of arrays: 9
>>
>> Array #1 ('GSM709330_HSB194-S1C-L') of 9...
>>
>> Adjusting PM signals only
>>
>> Obtaining signals...
>>
>> Obtaining signals...done
>>
>> Applying normal+exponential signal model...
>>
>> Applying normal+exponential signal model...done
>>
>> Writing adjusted probe signals...
>>
>>Adding temporary suffix from file...
>>
>> Pathname:
>> probeData/NIK_2014,RBC,coreR3/HuEx-1_0-st-v2/GSM709330_HSB194-S1C-L.CEL
>>
>> Suffix: .tmp
>>
>> Rename existing file?: FALSE
>>
>> Temporary pathname:
>> probeData/NIK_2014,RBC,coreR3/HuEx-1_0-st-v2/GSM709330_HSB194-S1C-L.CEL.tmp
>>
>>Adding temporary suffix from file...done
>>
>>Creating CEL file for results, if missing...
>>
>>Creating CEL file for results, if missing...done
>>
>>Writing adjusted intensities...
>>
>>Writing adjusted intensities...done
>>
>>Dropping temporary suffix from file...
>>
>> Temporary pathname:
>> probeData/NIK_2014,RBC,coreR3/HuEx-1_0-st-v2/GSM709330_HSB194-S1C-L.CEL.tmp
>>
>> Suffix: .tmp
>>
>> Regular expression for suffix: \.tmp$
>>
>> Pathname:
>> probeData/NIK_2014,RBC,coreR3/HuEx-1_0-st-v2/GSM709330_HSB194-S1C-L.CEL
>>
>> Renaming existing file...
>>
>> Result: TRUE
>>
>> Renaming existing file...done
>>
>>Dropping temporary suffix from file...done
>>
>> Writing adjusted probe signals...done
>>
>> used (Mb) gc trigger (Mb) max used (Mb)
>>
>> Ncells 709078 37.91166886 62.4 1166886 62.4
>>
>> Vcells 31586985 241.0 47054688 359.0 46991036 358.6
>>
>> AffymetrixCelFile:
>>
>> Name: GSM709330_HSB194-S1C-L
>>
>> Tags:
>>
>> Full name: GSM709330_HSB194-S1C-L
>>
>> Pathname:
>> probeData/NIK_2014,RBC,coreR3/HuEx-1_0-st-v2/GSM709330_HSB194-S1C-L.CEL
>>
>> File size: 62.73 MB (65775403 bytes)
>>
>> RAM: 0.00 MB
>>
>> File format: v4 (binary; XDA)
>>
>> Platform: Affymet
Re: [aroma.affymetrix] Error when analyzing CEL files using process() function: "No permission to modify existing file: /probeData..."
Hi,
good that it works for you with this workaround. The fix in aroma is
fairly simple(*). I'll let you know when an updated version is
available.
(*) DETAILS: This has to do with base::file.copy() and its argument
'copy.mode' which was introduced in R 2.13.0 (April 2011). The thing
is that they set the default to TRUE (whereas the previous behavior
was equivalent to FALSE), meaning any files copied will inherit the
file permissions from the source. Various steps in the aroma pipeline
*copies* the source CEL file and uses that as a template to store
updates signals. This is what hits you. I'll updating to make use of
base::file.copy(..., copy.mode=FALSE) such that one can work with also
read-only CEL files.
Thanks for reporting on this (not too unlikely) use case
Henrik
On Thu, Sep 4, 2014 at 1:35 PM, Taylor Raborn wrote:
> Hi Henrik:
>
> Thank you for the prompt reply. You are right- the .CEL files are all read
> only (see their permissions, below)
>
> rtraborn@Mason:
> /N/dc2/scratch/rtraborn/ML_Project/NIK_2014/rawData/NIK_2014/HuEx-1_0-st-v2>
> ls -lkhtra
>
>
> -r--r--r-- 1 ... 63M Jan 25 2011 GSM709338_HSB194-VFC-R.CEL
>
> -r--r--r-- 1 ... 63M Jan 25 2011 GSM709337_HSB194-VFC-L.CEL
>
> -r--r--r-- 1 ... 63M Jan 25 2011 GSM709336_HSB194-V1C-R.CEL
>
> -r--r--r-- 1 ... 63M Jan 25 2011 GSM709335_HSB194-V1C-L.CEL
>
> -r--r--r-- 1 ... 63M Jan 25 2011 GSM709334_HSB194-STR-L.CEL
>
> -r--r--r-- 1 ... 63M Jan 25 2011 GSM709333_HSB194-STC-R.CEL
>
> -r--r--r-- 1 ... 63M Jan 25 2011 GSM709332_HSB194-STC-L.CEL
>
> -r--r--r-- 1 ... 63M Jan 25 2011 GSM709331_HSB194-S1C-R.CEL
>
> -r--r--r-- 1 ... 63M Jan 25 2011 GSM709330_HSB194-S1C-L.CEL
>
>
> After changing the permissions, the job performed without issue (I'm showing
> you only the results of 1/9 for the sake of brevity):
>
>> csBC <- process(bc,verbose=verbose)
>
> Background correcting data set...
>
> Number of arrays: 9
>
> Array #1 ('GSM709330_HSB194-S1C-L') of 9...
>
> Adjusting PM signals only
>
> Obtaining signals...
>
> Obtaining signals...done
>
> Applying normal+exponential signal model...
>
> Applying normal+exponential signal model...done
>
> Writing adjusted probe signals...
>
>Adding temporary suffix from file...
>
> Pathname:
> probeData/NIK_2014,RBC,coreR3/HuEx-1_0-st-v2/GSM709330_HSB194-S1C-L.CEL
>
> Suffix: .tmp
>
> Rename existing file?: FALSE
>
> Temporary pathname:
> probeData/NIK_2014,RBC,coreR3/HuEx-1_0-st-v2/GSM709330_HSB194-S1C-L.CEL.tmp
>
>Adding temporary suffix from file...done
>
>Creating CEL file for results, if missing...
>
>Creating CEL file for results, if missing...done
>
>Writing adjusted intensities...
>
>Writing adjusted intensities...done
>
>Dropping temporary suffix from file...
>
> Temporary pathname:
> probeData/NIK_2014,RBC,coreR3/HuEx-1_0-st-v2/GSM709330_HSB194-S1C-L.CEL.tmp
>
> Suffix: .tmp
>
> Regular expression for suffix: \.tmp$
>
> Pathname:
> probeData/NIK_2014,RBC,coreR3/HuEx-1_0-st-v2/GSM709330_HSB194-S1C-L.CEL
>
> Renaming existing file...
>
> Result: TRUE
>
> Renaming existing file...done
>
>Dropping temporary suffix from file...done
>
> Writing adjusted probe signals...done
>
> used (Mb) gc trigger (Mb) max used (Mb)
>
> Ncells 709078 37.91166886 62.4 1166886 62.4
>
> Vcells 31586985 241.0 47054688 359.0 46991036 358.6
>
> AffymetrixCelFile:
>
> Name: GSM709330_HSB194-S1C-L
>
> Tags:
>
> Full name: GSM709330_HSB194-S1C-L
>
> Pathname:
> probeData/NIK_2014,RBC,coreR3/HuEx-1_0-st-v2/GSM709330_HSB194-S1C-L.CEL
>
> File size: 62.73 MB (65775403 bytes)
>
> RAM: 0.00 MB
>
> File format: v4 (binary; XDA)
>
> Platform: Affymetrix
>
> Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
>
> Timestamp: 2011-01-25 12:15:03
>
> Array #1 ('GSM709330_HSB194-S1C-L') of 9...done
>
>
> -
>
>
> There must be a file permissions transfer behavior that takes place on a
> multi-user cluster environment that doesn't take place on other types of
> machines, because I was unable to reproduce this error elsewhere. I didn't
> bother changing the raw .CEL files' permissions because I never experienced
> a problem of this nature with .CEL files.
>
>
> Let me know if you patch this up so I can pull the latest code from the
> aroma repo.
>
>
> Thanks for your help with this and for taking a look at the issue so
> quickly.
>
>
> Best regards,
>
>
> Taylor
>
>
>
Re: [aroma.affymetrix] Error when analyzing CEL files using process() function: "No permission to modify existing file: /probeData..."
Hi,
interesting. A quick guess is that the input file, i.e.
rawData/NIK_2014/HuEx-1_0-st-v2/GSM709330_HSB194-S1C-L.CEL
is write protected (e.g. file owned by someone else). This could be
the reason, because internally that file is copied and used as a
template and the copy may inherit the file permissions. What does ls
-l say about the above file?
If this is the case, I need to update the copying such that the new
file has proper permissions.
Thanks for the report
Henrik
On Thu, Sep 4, 2014 at 10:15 AM, Taylor Raborn wrote:
> Hi Henrik:
>
> I just come across an unusual error when using aroma.affymetrix on our
> high-memory HPC machine. It may or may not be platform-specific, and I'll
> give you all the information I can in the hopes of isolating and identifying
> the error.
>
> Traceback:
>
>> traceback()
>
> 18: stop(cond)
>
> 17: throw.Exception(Exception(...))
>
> 16: throw(Exception(...))
>
> 15: throw.default("No permission to modify existing file: ", pathname)
>
> 14: throw("No permission to modify existing file: ", pathname)
>
> 13: getWritablePathname.Arguments(static, ...)
>
> 12: getWritablePathname(static, ...) at #1
>
> 11: Arguments$getWritablePathname(pathname, mustExist = TRUE)
>
> 10: renameFile.default(srcPathname, pathname, ...)
>
> 9: renameFile(srcPathname, pathname, ...)
>
> 8: renameTo.GenericDataFile(res, filename = pathname, verbose =
> less(verbose))
>
> 7: renameTo(res, filename = pathname, verbose = less(verbose))
>
> 6: createFrom.AffymetrixCelFile(this, filename = pathnameT, path = NULL,
>
>verbose = less(verbose))
>
> 5: createFrom(this, filename = pathnameT, path = NULL, verbose =
> less(verbose))
>
> 4: bgAdjustRma.AffymetrixCelFile(df, path = outputPath, pmonly = pmonly,
>
>addJitter = addJitter, jitterSd = jitterSd, overwrite = force,
>
>verbose = verbose, .deprecated = FALSE)
>
> 3: bgAdjustRma(df, path = outputPath, pmonly = pmonly, addJitter =
> addJitter,
>
>jitterSd = jitterSd, overwrite = force, verbose = verbose,
>
>.deprecated = FALSE)
>
> 2: process.RmaBackgroundCorrection(bc, verbose = verbose)
>
> 1: process(bc, verbose = verbose)
>
>
>
>
> sessionInfo:
>
>> sessionInfo()
>
> R version 3.0.1 (2013-05-16)
>
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
>
> locale:
>
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>
> [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>
> [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>
> [7] LC_PAPER=C LC_NAME=C
>
> [9] LC_ADDRESS=C LC_TELEPHONE=C
>
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
>
> attached base packages:
>
> [1] tools parallel stats graphics grDevices utils datasets
>
> [8] methods base
>
>
> other attached packages:
>
> [1] R.cache_0.10.0 base64enc_0.1-2 aroma.apd_0.5.0
>
> [4] preprocessCore_1.24.0 affyio_1.30.0 Biobase_2.20.1
>
> [7] BiocGenerics_0.6.0 aroma.light_1.32.0 matrixStats_0.10.0
>
> [10] aroma.affymetrix_2.12.0 aroma.core_2.12.1 R.devices_2.11.0
>
> [13] R.filesets_2.6.0R.utils_1.33.0 R.oo_1.18.0
>
> [16] affxparser_1.34.2 affy_1.40.0 R.methodsS3_1.6.1
>
> [19] PSCBS_0.43.0DNAcopy_1.36.0 BiocInstaller_1.12.1
>
>
> loaded via a namespace (and not attached):
>
> [1] digest_0.6.4R.huge_0.8.0R.rsp_0.19.0zlibbioc_1.11.1
>
>
>
> Here's how I produced the error. Note that my directory structure matches
> that on the aroma-project.org site, shown here:
>
>> chipType <- "HuEx-1_0-st-v2"
>
>
>> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="coreR3,A20071112,EP")
>
>
>> print(cdf)
>
> AffymetrixCdfFile:
>
> Path: annotationData/chipTypes/HuEx-1_0-st-v2
>
> Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
>
> File size: 38.25 MB (40108891 bytes)
>
> Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
>
> RAM: 0.00MB
>
> File format: v4 (binary; XDA)
>
> Dimension: 2560x2560
>
> Number of cells: 6553600
>
> Number of units: 18708
>
> Cells per unit: 350.31
>
> Number of QC units: 1
>
>
>> cs <- AffymetrixCelSet$byName("NIK_2014", cdf=cdf)
>
>
>> print(cs)
>
> AffymetrixCelSet:
>
> Name: NIK_2014
>
> Tags:
>
> Path: rawData/NIK_2014/HuEx-1_0-st-v2
>
> Platform: Affymetrix
>
> Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
>
> Number of arrays: 9
>
> Names: GSM709330_HSB194-S1C-L, GSM709331_HSB194-S1C-R,
> GSM709332_HSB194-STC-L, ..., GSM709338_HSB194-VFC-R [9]
>
> Time period: 2011-01-25 12:15:03 -- 2011-01-25 13:48:02
>
> Total file size: 564.87MB
>
> RAM: 0.02MB
>
>
>> csBC <- process(bc,verbose=verbose)
>
> Background correcting data set...
>
> Number of arrays: 9
>
> Array #1 ('GSM709330_HSB194-S1C-L') of 9...
>
> Adjusting PM signals only
>
> Obtaining signals...
>
> Obtaining signals...done
>
> Applying normal+exponential signal model...
>
> Applying normal+exponential signal model...done
>
> Writing adjusted probe signals...
>
>Adding temporary s
Re: [aroma.affymetrix] normalization running for long time (>3 weeks)
Hi.
On Tue, Jun 24, 2014 at 8:45 AM, wrote:
> Hello,
>
> I have a large dataset of ~1 CEL files that needs to be normalized. I
> tried using aroma.affy for this, but the job is running for more than 3
> weeks and in need of help/suggestions. The data is in standard affy rat2302
> chip.
My first concern (more on this below): The formal Affymetrix name of
this *chip type* is not 'rat2302', but rather 'Rat230_2'
[http://aroma-project.org/chipTypes/Rat230_2]. It is very very ...
very important that you understand the difference between *chip type*
and *CDF*. If not, please spend a minute reading
http://aroma-project.org/definitions/chipTypesAndCDFs
> I steps I used are (based on:
> http://www.aroma-project.org/vignettes/GeneSTArrayAnalysis):
>
> library("aroma.affymetrix")
> library(rat2302cdf)
The Bioconductor package 'rat2302cdf' is *not* need by
aroma.affymetrix, nor used. You can skip loading it.
>
> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> chipType <- "rat2302"
> cdf <- AffymetrixCdfFile$byChipType(chipType) #, tags="r3")
Since you're using chip type 'rat2302' here I wonder where you got the
rat2302.CDF file from? It should have been named 'Rat230_2' if you
got it from Affymetrix.
Continuing, assuming that you got a hold of a proper Rat230_2 CDF file
and renamed it to 'rat2302' (not correct, but will work).
> cs <- AffymetrixCelSet$byName("tissues", cdf=cdf)
> bc <- RmaBackgroundCorrection(cs)
> csBC <- process(bc,verbose=verbose)
> qn <- QuantileNormalization(csBC, typesToUpdate="pm")
> csN <- process(qn, verbose=verbose)
>
> plm <- RmaPlm(csN)
> fit(plm, verbose=verbose)
>
> All steps were ok but the last step : fit(plm,verbose=verbose) is running
> for nearly 3 weeks. Is this needed for probe summarization? What exactly
> does this fit do?
Yes, probe summarization is definitely needed and is a fundamental
concept/step in almost all Affymetrix microarray analyses. Google
'Affymetrix probe summarization' or 'Affymetrix RMA' and you should
gets heaps of references.
>
> Any suggestion will be helpful.
Have a look here: http://aroma-project.org/howtos/ImproveProcessingTime
Despite the title, the following thread should also be informative and
helpful for speeding up probe summarization:
aroma.affymetrix, Speeding up RmaBackgroundCorrection, started 2014-02-16
https://groups.google.com/forum/#!msg/aroma-affymetrix/U2MGe9778JI/IyzXk0GJnZQJ
See my reply on March 7.
Hope this helps
Henrik
>
> Thanks,
> Rafi
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
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>
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Re: [aroma.affymetrix] read in CEL.gz files
Hi, slow response but answers below.
On Wed, Apr 2, 2014 at 8:20 AM, hr wrote:
> Dear Henrik,
>
> Is there a way to read in CEL.gz files rather than .CEL files?
Unfortunately not, only non-compressed CEL files are supported. This
is mainly because the Affymetrix Fusion SDK that we utilize via the
'affxparser' package does not support compressed files.
>
> Also, do you provide an example (couldn't find one on the aroma homepage) on
> how to go from a CDF file and a bunch of CEL files to a final expression
> matrix normalized with RMA? Essentially I am looking for the equivalent of:
>
>
> library(affy)
> library(annotate)
> library(hgu133plus2.db)
>
> files = c("A.CEL.gz", "B.CEL.gz", "C.CEL.gz")
> setwd("datadir")
>
> eset <- justRMA(filenames = files)
> mat <- exprs(eset)
>
>
> What is the most efficient way to do this with Aroma?
I've added justRMA() to aroma.affymetrix 2.12.2 so you can do:
cs <- AffymetrixCelSet$byName("AbcDataSet", chipType="HG-U133_Plus_2")
eset <- justRMA(cs)
mat <- exprs(eset)
which replicates affy::justRMA() very well. This is done keeping the
memory usage constant regardless of the number of arrays during the
preprocessing. At the end, before justRMA() returns a
Biobase::ExpressionSet it needs to load the *summarized* data in, so
then memory becomes an issue, but that hits you order of magnitudes
later compared to the probe-level data. For example, on
HG-U133_Plus_2 there is 54,675 units and 'eset' contains both signals
and standard errors (8+8 bytes), so one array requires ~0.84 MB of
RAM. Thus, 1,000 arrays occupies roughly 0.84 GB of RAM. To
efficiently being able to manipulate in Bioconductor, you should
double or triple the memory requirements.
You can install/update to the most recent version of aroma.affymetrix as:
source('http://aroma-project.org/R/install#aroma.affymetrix')
Hope this helps
Henrik
>
> Many thanks and best wishes!
>
> Helge
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
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>
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Re: [aroma.affymetrix] NA values in aroma.affymetrix
Hi, considered that there are lots and lots of functions in aroma.affymetrix your questions is a bit vague, but if your thinking of missing values in probe signals, then yes, such probes are "ignored" and won't affect the estimates. /Henrik On Sun, May 25, 2014 at 9:50 AM, wrote: > hello everybody > i have a question > does ignore aroma.affymetrix NA values in its computations? > thank for answers > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the > latest version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to > http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] CYTOSCAN HD Analysis using PSCBS
Hi. On Fri, May 16, 2014 at 1:23 AM, Farhan Haq wrote: > Hello, > > I have two questions regarding cnv analysis using CytoscanHD data. > > 1) > > I am currently implementing PSCBS on my Cancer datasets. This tool looks > quite interesting to me. > > However, what to do you say about giving exact values for calling copy > number gains and losses? Can you suggest any thresholds? Any values above 4 > would be high copy gains and near zero would be deletions? Unfortunately, it does not work to call CN states by predetermined thresholds. The thresholds are sample specific and depends on such things as normal contamination, tumor heterogeneity and artificial compression introduced by the assay/technology. Calling CN states is very hard and I still haven't seen a caller that works satisfactory. > > I have a dataset of more than 200 hundred lung cancer samples so I want to > apply significant testing on cnvs. Does GISTIC type algorithms will work on > the attached example file? Or any other method you suggest I don't remember the details on GISTIC and what file format it accepts. What I know is that output format of PSCBS was *not* specifically designed to work with GISTIC, so it may or may not work out of the box. Otherwise, it shouldn't be too hard for someone who knows a little bit of programming to transform the file to something that GISTIC understands. > > > 2) > > Is tumorboost works with cytoscanHD data? Yes - TumorBoost can normalize any matched tumor-normal CN data regardless of chip type. Hope this helps Henrik > > Thanks > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] Re: Problem in MSCN : Error in smooth.spline(sKK, lambda, ...)
On Sat, May 3, 2014 at 10:20 PM, Clara Tang wrote:
> Thanks so much for your advice. I have now upgraded the R to the latest
> version and reinstall the aroma libraries. Do I need to rerun all
> procedures, e.g. crmav2, or simply the mscn?
No need to rerun the CRMAv2 pipeline - those results are unaffected by
that bug. (BTW, by the nature of aroma, if you did, aroma would
quickly skip over already processed parts so in the end of the day it
doesn't matter).
/Henrik
>
> Regards,
> Clara
>
> On Sunday, April 27, 2014 5:35:47 PM UTC+8, Clara Tang wrote:
>>
>> Hi,
>>
>> I am trying to perform cross platform normalization for CytoScan and Omni
>> using MSCN but the program stops after smoothing. I imported the Affymetrix
>> raw intensity data and called the totalCn and Baf using CRMAv2 and CalMate.
>> LogR ratio (log2 scale) and BAF were extracted using GenomeStudio for Omni
>> and imported as 2^LRR*2 and BAF into .total.asb and .fracB.asb respectively.
>> Plotting the CN indicated similar level of mean intensities for both
>> platforms (CN~1) and thereby I proceeded to perform the mscn. Smoothing
>> looks normal but after that, the program seemed to stop while
>> backtransforming.
>>
>> May I know how I can overcome the error of smooth.spline(sKK, lambda,
>> ...)?? What's wrong in my data?
>>
>> Thanks a lot!!
>>
>> --Clara
>>
>> P.S. Log file is pasted as below,
>>
>> =
>> dsNList <- process(mscn, verbose=log)
>> 20140427 17:06:46|Multi-source normalize all samples...
>> 20140427 17:06:46| Number of unique samples in all sets: 8
>> chr [1:8] "9C" "9C-2" "2C" "2C-2" "4C" ...
>> 20140427 17:06:46| Processing each array...
>> 20140427 17:06:46| Sample #1 ('9C') of 8...
>> 20140427 17:06:46| Identifying source data files...
>> 20140427 17:06:46|Getting list tuple of data files for one sample...
>> 20140427 17:06:46| Sample name: 9C
>> 20140427 17:06:47| Number of arrays: 2
>> 20140427 17:06:47|Getting list tuple of data files for one
>> sample...done
>> [[1]]
>> AromaUnitTotalCnBinaryFile:
>> Name: 9C
>> Tags: total
>> Full name: 9C,total
>> Pathname:
>> totalAndFracBData/Cytoscan,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,CMTN,v2/CytoScanHD_Array/9C,total.asb
>> File size: 10.77 MB (11288937 bytes)
>> RAM: 0.01 MB
>> Number of data rows: 2822125
>> File format: v1
>> Dimensions: 2822125x1
>> Column classes: double
>> Number of bytes per column: 4
>> Footer: 20140421 18:35:53
>> HKTAffymetrixCytoScanHD_ArrayCytoscan,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XYCytoScanHD_Array,monocell9C,chipEffects7d70e31c6aa60b7d866437ad5452
>> Platform: Affymetrix
>> Chip type: CytoScanHD_Array
>>
>> [[2]]
>> AromaUnitTotalCnBinaryFile:
>> Name: 9C
>> Tags:9C,ratio,total
>> Full name: 9C,9C,ratio,total
>> Pathname: totalAndFracBData/Omni/HumanOmni2.5/9C,9C,ratio,total.asb
>> File size: 9.08 MB (9519600 bytes)
>> RAM: 0.01 MB
>> Number of data rows: 2379855
>> File format: v1
>> Dimensions: 2379855x1
>> Column classes: double
>> Number of bytes per column: 4
>> Footer: 20140427 16:14:31
>> HKTIlluminaHumanOmni2.5
>> Platform: Illumina
>> Chip type: HumanOmni2.5
>>
>> 20140427 17:06:47| Identifying source data files...done
>> 20140427 17:06:47| Check if all arrays are already normalized...
>> 20140427 17:06:47|Is done: FALSE
>> 20140427 17:06:47| Check if all arrays are already normalized...done
>> 20140427 17:06:47| Fitting model...
>> 20140427 17:06:47|Fitting one sample across multiple sources...
>> 20140427 17:06:47| Number of arrays: 2
>> 20140427 17:06:47| Sample name: 9C
>> List of 4
>> $ subsetToFit: int [1:28781] 1 2 3 4 5 6 7 8 9 10 ...
>> $ fitUgp :Classes 'AromaUgpFile',
>> 'AromaUnitChromosomeTabularBinaryFile', 'AromaUnitTabularBinaryFile',
>> 'UnitAnnotationDataFile', 'AromaMicroarrayTabularBinaryFile',
>> 'AromaPlatformInterface', 'AromaTabularBinaryFile', 'FileCacheKeyInterface',
>> 'CacheKeyInterface', 'GenericTabularFile', 'ColumnNamesInterface',
>> 'GenericDataFile', 'FullNameInterface', 'Object' atomic [1:1] NA
>>.. ..- attr(*, ".env")=
>> $ align : chr "byChromosome"
>> $ targetDimension: int 1
>> 20140427 17:06:47| Getting list tuple of data files for one sample...
>> 20140427 17:06:47| Sample name: 9C
>> 20140427 17:06:47| Number of arrays: 2
>> 20140427 17:06:47| Getting list tuple of data files for one
>> sample...done
>> List of 2
>> $ :Classes 'AromaUnitTotalCnBinaryFile', 'CopyNumberDataFile',
>> 'AromaUnitSignalBinaryFile', 'AromaPlatformInterface',
>> 'AromaTabularBinaryFile', 'FileCacheKeyInterface', 'CacheKeyInterface',
>> 'GenericTabularFile', 'ColumnNamesInterface', 'GenericDataFile',
>> 'FullNameInterface', 'Object' atomic [1:1] NA
>>.. ..- attr(*, ".env")=
>> $ :Classes 'AromaUnitTot
Re: [aroma.affymetrix] Re: Problem in MSCN : Error in smooth.spline(sKK, lambda, ...)
Hi,
it turns out that this was fixed in aroma.light v1.30.1(*). Now,
aroma.light (>= 1.30.1) is part of Bioc v2.12 which is for R (>=
3.0.0). You are using R 2.15.1. So, in order for you do fix this
problem, you have to upgrade R. This is something you should either
way, because during the last 2 years lots of things have improved,
several bug have been fixed and so on (both in R, BioC and aroma).
Current stable release is R 3.1.0 (April 2014). Also, the next
release of aroma.affymetrix et al. will require at least R (>= 3.0.1).
(*) Details from news(package="aroma.light"):
Version: 1.30.1 [2013-04-18]:
o BUG FIX: backtransformPrincipalCurve() gave an error if the
pricipal curve was fitted using data with missing values.
Hope this helps
Henrik
On Fri, May 2, 2014 at 1:33 AM, Clara Tang wrote:
> Dear Henrik,
>
> Thanks for your prompt reply. When I type sessionInfo(), the output is as
> follows,
>
>>sessionInfo()
>
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_HK.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_HK.UTF-8LC_COLLATE=en_HK.UTF-8
> [5] LC_MONETARY=en_HK.UTF-8LC_MESSAGES=en_HK.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_HK.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] aroma.affymetrix_2.12.0 aroma.light_1.24.0 aroma.cn_1.5.0
> [4] aroma.core_2.12.1 R.devices_2.8.2 R.filesets_2.4.0
> [7] R.utils_1.29.8 R.oo_1.18.0 affxparser_1.28.1
> [10] R.methodsS3_1.6.1
>
> loaded via a namespace (and not attached):
> [1] aroma.apd_0.5.0base64enc_0.1-1digest_0.6.4 DNAcopy_1.30.0
> [5] matrixStats_0.8.14 PSCBS_0.40.4 R.cache_0.9.2 R.huge_0.8.0
> [9] R.rsp_0.15.0 tools_2.15.1
>
> Is there any problem with the version of Aroma files? I just updated them
> recently but the workspace was built a while ago.
>
> Regards,
> Clara
>
>
> On Sunday, April 27, 2014 5:35:47 PM UTC+8, Clara Tang wrote:
>>
>> Hi,
>>
>> I am trying to perform cross platform normalization for CytoScan and Omni
>> using MSCN but the program stops after smoothing. I imported the Affymetrix
>> raw intensity data and called the totalCn and Baf using CRMAv2 and CalMate.
>> LogR ratio (log2 scale) and BAF were extracted using GenomeStudio for Omni
>> and imported as 2^LRR*2 and BAF into .total.asb and .fracB.asb respectively.
>> Plotting the CN indicated similar level of mean intensities for both
>> platforms (CN~1) and thereby I proceeded to perform the mscn. Smoothing
>> looks normal but after that, the program seemed to stop while
>> backtransforming.
>>
>> May I know how I can overcome the error of smooth.spline(sKK, lambda,
>> ...)?? What's wrong in my data?
>>
>> Thanks a lot!!
>>
>> --Clara
>>
>> P.S. Log file is pasted as below,
>>
>> =
>> dsNList <- process(mscn, verbose=log)
>> 20140427 17:06:46|Multi-source normalize all samples...
>> 20140427 17:06:46| Number of unique samples in all sets: 8
>> chr [1:8] "9C" "9C-2" "2C" "2C-2" "4C" ...
>> 20140427 17:06:46| Processing each array...
>> 20140427 17:06:46| Sample #1 ('9C') of 8...
>> 20140427 17:06:46| Identifying source data files...
>> 20140427 17:06:46|Getting list tuple of data files for one sample...
>> 20140427 17:06:46| Sample name: 9C
>> 20140427 17:06:47| Number of arrays: 2
>> 20140427 17:06:47|Getting list tuple of data files for one
>> sample...done
>> [[1]]
>> AromaUnitTotalCnBinaryFile:
>> Name: 9C
>> Tags: total
>> Full name: 9C,total
>> Pathname:
>> totalAndFracBData/Cytoscan,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,CMTN,v2/CytoScanHD_Array/9C,total.asb
>> File size: 10.77 MB (11288937 bytes)
>> RAM: 0.01 MB
>> Number of data rows: 2822125
>> File format: v1
>> Dimensions: 2822125x1
>> Column classes: double
>> Number of bytes per column: 4
>> Footer: 20140421 18:35:53
>> HKTAffymetrixCytoScanHD_ArrayCytoscan,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XYCytoScanHD_Array,monocell9C,chipEffects7d70e31c6aa60b7d866437ad5452
>> Platform: Affymetrix
>> Chip type: CytoScanHD_Array
>>
>> [[2]]
>> AromaUnitTotalCnBinaryFile:
>> Name: 9C
>> Tags:9C,ratio,total
>> Full name: 9C,9C,ratio,total
>> Pathname: totalAndFracBData/Omni/HumanOmni2.5/9C,9C,ratio,total.asb
>> File size: 9.08 MB (9519600 bytes)
>> RAM: 0.01 MB
>> Number of data rows: 2379855
>> File format: v1
>> Dimensions: 2379855x1
>> Column classes: double
>> Number of bytes per column: 4
>> Footer: 20140427 16:14:31
>> HKTIlluminaHumanOmni2.5
>> Platform: Illumina
>> Chip type: HumanOmni2.5
>>
>> 20140427 17:06:47| Identifying source data files...done
>> 20140427 17:06:47| Check if all arrays a
Re: [aroma.affymetrix] Problem in MSCN : Error in smooth.spline(sKK, lambda, ...)
Hi,
before anything else, what's your sessionInfo() after
library("aroma.affymetrix")?
/Henrik
On Sun, Apr 27, 2014 at 2:35 AM, Clara Tang wrote:
> Hi,
>
> I am trying to perform cross platform normalization for CytoScan and Omni
> using MSCN but the program stops after smoothing. I imported the Affymetrix
> raw intensity data and called the totalCn and Baf using CRMAv2 and CalMate.
> LogR ratio (log2 scale) and BAF were extracted using GenomeStudio for Omni
> and imported as 2^LRR*2 and BAF into .total.asb and .fracB.asb respectively.
> Plotting the CN indicated similar level of mean intensities for both
> platforms (CN~1) and thereby I proceeded to perform the mscn. Smoothing
> looks normal but after that, the program seemed to stop while
> backtransforming.
>
> May I know how I can overcome the error of smooth.spline(sKK, lambda,
> ...)?? What's wrong in my data?
>
> Thanks a lot!!
>
> --Clara
>
> P.S. Log file is pasted as below,
>
> =
> dsNList <- process(mscn, verbose=log)
> 20140427 17:06:46|Multi-source normalize all samples...
> 20140427 17:06:46| Number of unique samples in all sets: 8
> chr [1:8] "9C" "9C-2" "2C" "2C-2" "4C" ...
> 20140427 17:06:46| Processing each array...
> 20140427 17:06:46| Sample #1 ('9C') of 8...
> 20140427 17:06:46| Identifying source data files...
> 20140427 17:06:46|Getting list tuple of data files for one sample...
> 20140427 17:06:46| Sample name: 9C
> 20140427 17:06:47| Number of arrays: 2
> 20140427 17:06:47|Getting list tuple of data files for one sample...done
> [[1]]
> AromaUnitTotalCnBinaryFile:
> Name: 9C
> Tags: total
> Full name: 9C,total
> Pathname:
> totalAndFracBData/Cytoscan,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,CMTN,v2/CytoScanHD_Array/9C,total.asb
> File size: 10.77 MB (11288937 bytes)
> RAM: 0.01 MB
> Number of data rows: 2822125
> File format: v1
> Dimensions: 2822125x1
> Column classes: double
> Number of bytes per column: 4
> Footer: 20140421 18:35:53
> HKTAffymetrixCytoScanHD_ArrayCytoscan,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XYCytoScanHD_Array,monocell9C,chipEffects7d70e31c6aa60b7d866437ad5452
> Platform: Affymetrix
> Chip type: CytoScanHD_Array
>
> [[2]]
> AromaUnitTotalCnBinaryFile:
> Name: 9C
> Tags:9C,ratio,total
> Full name: 9C,9C,ratio,total
> Pathname: totalAndFracBData/Omni/HumanOmni2.5/9C,9C,ratio,total.asb
> File size: 9.08 MB (9519600 bytes)
> RAM: 0.01 MB
> Number of data rows: 2379855
> File format: v1
> Dimensions: 2379855x1
> Column classes: double
> Number of bytes per column: 4
> Footer: 20140427 16:14:31
> HKTIlluminaHumanOmni2.5
> Platform: Illumina
> Chip type: HumanOmni2.5
>
> 20140427 17:06:47| Identifying source data files...done
> 20140427 17:06:47| Check if all arrays are already normalized...
> 20140427 17:06:47|Is done: FALSE
> 20140427 17:06:47| Check if all arrays are already normalized...done
> 20140427 17:06:47| Fitting model...
> 20140427 17:06:47|Fitting one sample across multiple sources...
> 20140427 17:06:47| Number of arrays: 2
> 20140427 17:06:47| Sample name: 9C
> List of 4
> $ subsetToFit: int [1:28781] 1 2 3 4 5 6 7 8 9 10 ...
> $ fitUgp :Classes 'AromaUgpFile',
> 'AromaUnitChromosomeTabularBinaryFile', 'AromaUnitTabularBinaryFile',
> 'UnitAnnotationDataFile', 'AromaMicroarrayTabularBinaryFile',
> 'AromaPlatformInterface', 'AromaTabularBinaryFile', 'FileCacheKeyInterface',
> 'CacheKeyInterface', 'GenericTabularFile', 'ColumnNamesInterface',
> 'GenericDataFile', 'FullNameInterface', 'Object' atomic [1:1] NA
>.. ..- attr(*, ".env")=
> $ align : chr "byChromosome"
> $ targetDimension: int 1
> 20140427 17:06:47| Getting list tuple of data files for one sample...
> 20140427 17:06:47| Sample name: 9C
> 20140427 17:06:47| Number of arrays: 2
> 20140427 17:06:47| Getting list tuple of data files for one
> sample...done
> List of 2
> $ :Classes 'AromaUnitTotalCnBinaryFile', 'CopyNumberDataFile',
> 'AromaUnitSignalBinaryFile', 'AromaPlatformInterface',
> 'AromaTabularBinaryFile', 'FileCacheKeyInterface', 'CacheKeyInterface',
> 'GenericTabularFile', 'ColumnNamesInterface', 'GenericDataFile',
> 'FullNameInterface', 'Object' atomic [1:1] NA
>.. ..- attr(*, ".env")=
> $ :Classes 'AromaUnitTotalCnBinaryFile', 'CopyNumberDataFile',
> 'AromaUnitSignalBinaryFile', 'AromaPlatformInterface',
> 'AromaTabularBinaryFile', 'FileCacheKeyInterface', 'CacheKeyInterface',
> 'GenericTabularFile', 'ColumnNamesInterface', 'GenericDataFile',
> 'FullNameInterface', 'Object' atomic [1:1] NA
>.. ..- attr(*, ".env")=
> 20140427 17:06:47| Extracting data...
> 20140427 17:06:47| Subset of units used for fitting:
>int [1:28781] 1 2 3 4 5 6 7 8 9 10 ...
>num [1:28781, 1:2] 0.561 0.566 0.798 0.8
Re: [aroma.affymetrix] CRMA v2 error with Mouse Diversity
Hi,
sorry for the wait - I missed this one. Before anything else, in your
script you are using the ACNE pipeline not the CRMAv2. You are saying
"I followed CRMA v2 vignette" - please let me know where you found
that, because if there's a document out there claiming to be CRMAv2
when it's using ACNE, it needs to be fixed.
So, the error originates from NmfSnpPlm, which is part of ACNE not
CRMAv2. I'm happy to help you troubleshoot why NmfSnpPlm complaints,
but then I would need to get the problematic data from you. However,
if you don't mind (allele-specific) CRMAv2 (I use it all the time
myself), then replace everything in the "Probe-processing as in CRMA
v2" section (AllelicCrosstalkCalibration() to getChipEffectSet()) in
your script with:
res <- doASCRMAv2(cs, drop=FALSE, verbose=verbose)
ces <- res$cesN
and then continue as before.
The 'ces' is an CnChipEffectSet object. It should have tags
ACC,-XY,BPN,-XY,AVG,FLN,-XY indicating that (i) allelic crosstalk has
been fitted to all chromosomes by X and Y and applied to all signals
(ACC,-XY), (ii) likewise for base-position normalization (BPN,-XY),
followed by (iii) allele-specific probe summarization using robust
averging (AVG), and finally (iv) fragment-length normalization fitted
to all but X and Y chromosomes and applied to all signals (FLN,-XY).
BTW, the steps done before NmfSnpPlm are the same, so those will be
picked up/won't have to be redone by CRMAv2.
Hope this helps
Henrik
On Tue, Mar 25, 2014 at 11:25 AM, wrote:
> Dear Sir or Madam,
>
> I would like to analyse Affymetrix Mouse Diversity Array, extract BAF LRR
> using CRMA v2
> I followed CRMA v2 vignette, and I get always an error during process() :
>
> ---
> 20140319 18:52:29| Reading probe intensities from 17 arrays...done
> 20140319 18:52:29| Fitting probe-level model...
> 20140319 18:52:29| Calling fitUnit() via lapply()
> Erreur dans if (sampleAA * sampleBB > 0L) { :
> l'argument est de longueur nulle
> Calls: fit ... fit.ProbeLevelModel -> -> FUN -> nmfFcn ->
> robustWInit
> De plus : Il y a eu 45 avis (utilisez warnings() pour les visionner)
> 20140319 18:55:34| Fitting probe-level model...done
> 20140319 18:55:34| Fitting chunk #1 of 6 of 'genotyping' units (code=2)
> with 4 groups/2+2+2+2 cells...done
> 20140319 18:55:34|Unit dimension #1 (4 groups/2+2+2+2 cells) of 4...done
> 20140319 18:55:34| Fitting the model by unit dimensions (at least for the
> large classes)...done
> 20140319 18:55:34| Unit type #2 ('genotyping') of 2...done
> 20140319 18:55:34| Fitting NmfSnpPlm for each unit type separately...done
> 20140319 18:55:34|Fitting model of class NmfSnpPlm...done
> Exécution arrêtée
>
>
> All packages are updated with the latest releases.
>
> here is sessionInfo()
> http://eric.voirin.free.fr/aroma/sessionInfo.Rout
>
> here is the script
> http://eric.voirin.free.fr/aroma/script_aroma.R
>
> here is the logfile
> http://eric.voirin.free.fr/aroma/script_aroma.Rout
>
> Easy to reprodruce.
> Thanks in advance for your time and ideas...
>
> Eric
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
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--
--
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version of the package, 2) to report the output of sessionInfo() and
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Re: [aroma.affymetrix] Doubts in PSCBS segments
Hi again.
Yes, it's odd to the eye that PSCBS fail to segment this sample; it
looks as it should pick it up at either the TCN or the following DH
segmentation step. My guess is that it fails to detect the change
point it in the TCN step is that there are enough outliers to mess up
the underlying assumption of a well behaving Gaussian distribution.
If you drop TCN outliers before calling the segmentation method, it
does work as expected, e.g.
data <- read.table("chr20_fail.csv", sep="\t", dec=",", header=TRUE)
data <- dropSegmentationOutliers(data)
fit <- segmentByPairedPSCBS(data)
Dropping TCN outliers is discussed in the 'Parent-specific copy-number
segmentation using Paired PSCBS' vignette part of the package
[http://cran.r-project.org/web/packages/PSCBS]. There we write that
the step is optional, but maybe should also write that we recommend it
(we use it all the time ourselves). BTW, in the same document, we
also show how to avoid segmenting over centromeres, e.g.
data <- read.table("chr20_fail.csv", sep="\t", dec=",", header=TRUE)
data <- dropSegmentationOutliers(data)
gaps <- findLargeGaps(data, minLength=1e+06)
knownSegments <- gapsToSegments(gaps)
fit <- segmentByPairedPSCBS(data, knownSegments=knownSegments)
Hope this helps
Henrik
On Thu, Apr 17, 2014 at 3:20 AM, Juan José Lozano Salvatella
wrote:
> Hi Henrik
>
> Thanks for your help!!
>
> Yes, the data.frame before PSCBS are different. Attached chr20 files from
> the good and bad results.
>
> Anyway, when you plot both results you can reproduce the plots...
>
> the only difference is the dataSet <- "RM";
>
> diff rLOH_CRC37_fail.r rLOH_CRC37.r
>
> 6c6
> < dataSet <- "RM";
> ---
>> dataSet <- "lite";
>
> In any case i think PSCBS must to segment better the "fail" version...at
> least at the cnv level
>
> Best
>
> Juanjo
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> El jueves, 17 de abril de 2014 02:22:58 UTC+2, Henrik Bengtsson escribió:
>>
>> On Wed, Apr 16, 2014 at 5:44 AM, Juan José Lozano Salvatella
>> wrote:
>> > Hi Henrik
>> >
>> > Thanks!! I understand. It seems X-files. I dont known what happens
>> > because i
>> > use the same script. May be the problem is related to past reruns in
>> > other
>> > computer (and probably other versions).
>>
>> I'm sure there are no aliens or higher powers involved; instead
>> there's probably a very simple answer to this.
>>
>> >
>> > When i use the script in a new rawdata folder (moving the cels and thus
>> > no
>> > using probedata and other temporary directories)
>> > the results are the expected.
>>
>> The way I read this is that you are forcing a new AS-CRMAv2 run.
>> Since AS-CRMAv2 is completely deterministic, I don't see how this
>> makes a difference. I still also don't understand if you are saying
>> whether this solved your problem? Can you still reproduce the
>> original problem or is appearing "randomly"?
>>
>> Looking at your two (Chr20) plots that you've sent,
>> 'double_problem_cnv.png' and 'file_corrected.png' it doesn't look like
>> to raw data is the same. So, to simplify your life, you could start
>> by asserting that you get the exact same 'data' object when you rerun
>> AS-CRMAv2. If that is not the case, the problem is unrelated to PSCBS
>> and that should be troubleshooted first.
>>
>> I would save 'data' after these steps:
>>
>> data <- extractPSCNArray(res$total);
>> dimnames(data)[[3]] <- names(pair);
>> saveObject(data, "data-run1.Rbin")
>>
>> then re-run in a different directory and save as:
>>
>> saveObject(data, "data-run2.Rbin")
>>
>> then you can compare the two outputs:
>>
>> library("R.utils")
>> data1 <- loadObject("data-run1.Rbin")
>> data2 <- loadObject("data-run2.Rbin")
>> stopifnot(all.equal(data1, data2))
>>
>> As a I said above, I would be surprised if you don't get that 'data1'
>> and 'data2' are equal/identical.
>>
>> /Henrik
>>
>> >
>> > Yes, i will check the pscbs vignette.
>> >
>> > Best
>> >
>> > Juanjo
>> >
>> >
>> > El martes, 15 de abril de 2014 18:43:42 UTC+2, Henrik Bengtsson
>> > escribió:
>> >>
>> >&
