[aroma.affymetrix] Re: cant get aroma to load
Thanks for reporting. Retry with:
if (.Platform$OS.type == "windows") options(url.method = "libcurl")
source("https://callr.org/install#aroma.affymetrix";)
We've updated the online installation instruction accordingly.
On Thursday, October 31, 2019 at 6:06:43 AM UTC+1, Sreya Mukherjee wrote:
>
> i get the following error. please help
>
> *source('https://callr.org/install#aroma.affymetrix
> ')*
> *Error in file(filename, "r", encoding = encoding) : *
> * cannot open the connection*
> *In addition: Warning message:*
> *In file(filename, "r", encoding = encoding) :*
> * cannot open URL 'https://callr.org/install#aroma.affymetrix
> ': HTTP status was '400 Bad
> Request'*
>
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Re: [aroma.affymetrix] Dealing with batches
Dear Peter, First, just to make sure we are talking about the same things, when you write "I have applied ASCRMA to each array separately.", you mean that you applied ASCRMA(v2) to each of the two *batches* separately, right ? In the aroma-project world, we usually reserve the word 'array' for what you called a 'sample'. Then, let me recall or clarify that ASCRMA(v2) processes each or the 28 samples separately. Therefore, it would make no difference you applied ASCRMAv2 on a single data set of 28 samples, or to two separate data sets, ...or to 28 separate data sets. This is why ASCRMA(v2) is called a "single-array" method. >From the density plots, it seems to me that the normalization was able to make the intensity distributions more similar, which is a good sign that part of the experimental variability has been removed. However, I would like to emphasize that we do not expect these distributions to be strictly identical after normalization (as would be the case if we were performing quantile normalization). In fact, some of the differences we see after normalization may correspond to true biological signal. At first sight it seems to me that it is safe to use your normalized data for downstream analysis. If you want to dig further, one thing you could do is to plot these densities for the normal samples only. There, we do not expect much biological variation in the densities. If there is still clear variation between the two batches, then one possibility to reduce it could be to force the "average" density of the normal samples of the two batches to be identical. The transformation used for the normal samples of each batch could then be used to normalize the other samples of that batch. I hope this will help you. Best, Pierre On Tue, Jan 5, 2016 at 7:32 AM, Peter Savas wrote: > Dear Group, > > I have 28 samples of tumour normal pairs, run on 2 GenomeWideSNP6.0 arrays > several months apart. Some of the pairs have members on different chips (ie > tumor on one, normal on the other). I am not sure about the best way to > normalise the data such that these split pairs can be used for downstream > analysis. The plan is for ASCRMA, TumorBoost and then PSCBS. > > I have applied ASCRMA to each array separately. Probe density plots pre and > post this normalisation are attached. It seems that there is still some room > for improvement. > > Thank you and all the best for the new year. > > Regards, > Peter > > -- > -- > 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] Error in readCelHeader(pathname) : Argument 'filename' should be a single file ..
Hi,
Could you also send a code example that generated this error ? From
what you sent there is no way to know what you did that generated this
error.
Best,
Pierre
On Fri, Jan 31, 2014 at 9:24 AM, wrote:
> Hello sir,
>
> i am getting following error. i am giving session info() and traceback ()
> i have tried many option..differrnt system and file name but all failed
> Please help me .Previously i was able to run sucessfully . But now i am
> facing the problem
>
>> traceback()
> 31: stop("Argument 'filename' should be a single file: ", paste(filename,
> collapse = ", "))
> 30: readCelHeader(pathname)
> 29: getHeader.AffymetrixCelFile(this)
> 28: getHeader(this)
> 27: getCdf.AffymetrixCelFile(getOneFile(this), ...)
> 26: getCdf(getOneFile(this), ...)
> 25: getCdf.AffymetrixCelSet(this)
> 24: getCdf(this)
> 23: clearCache.AffymetrixCelSet(object)
> 22: clearCache(object)
> 21: clone.GenericDataFileSet(this, clear = TRUE, verbose = FALSE)
> 20: NextMethod("clone", clear = TRUE, verbose = less(verbose))
> 19: clone.AffymetrixCelSet(this)
> 18: clone(this)
> 17: extract.GenericDataFileSet(dsOut, fullnames, onMissing = onMissing)
> 16: extract(dsOut, fullnames, onMissing = onMissing)
> 15: getOutputDataSet.AromaTransform(this, incomplete = TRUE, ...,
> verbose = less(verbose, 5), cdf = NA, checkChipType = FALSE)
> 14: NextMethod(generic = "getOutputDataSet", NA, incomplete = TRUE,
> cdf = NA, checkChipType = FALSE, verbose = FALSE)
> 13: do.call("NextMethod", args)
> 12: getOutputDataSet.Transform(this, incomplete = TRUE, ..., verbose =
> less(verbose,
> 5))
> 11: getOutputDataSet(this, incomplete = TRUE, ..., verbose = less(verbose,
> 5))
> 10: findFilesTodo.AromaTransform(this, ...)
> 9: findFilesTodo(this, ...)
> 8: isDone.AromaTransform(this)
> 7: isDone(this)
> 6: sprintf("Is done: %s", isDone(this))
> 5: as.character.AromaTransform(x)
> 4: as.character(x)
> 3: print(as.character(x))
> 2: print.Object(NA)
> 1: print(NA)
>> rs
> Error: object 'rs' not found
>> sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252
> [3] LC_MONETARY=English_India.1252 LC_NUMERIC=C
> [5] LC_TIME=English_India.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] aroma.light_1.32.0 matrixStats_0.8.14 aroma.affymetrix_2.11.1
> [4] aroma.core_2.11.3 R.devices_2.8.2 R.filesets_2.3.0
> [7] R.utils_1.29.1 R.oo_1.17.0 affxparser_1.34.0
> [10] R.methodsS3_1.6.1
>
> loaded via a namespace (and not attached):
> [1] aroma.apd_0.4.0 base64enc_0.1-1 digest_0.6.4DNAcopy_1.36.0
> [5] PSCBS_0.40.3R.cache_0.9.2 R.huge_0.6.0R.rsp_0.9.28
> [9] tools_3.0.2
>>
>
> --
> --
> 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.
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Re: [aroma.affymetrix] "Cannot fit normalization function to enzyme" error
Hi Z., If you want people to be able to help you out, then you need to explain exactly what you did. Can you report the output of sessionInfo() and traceback(), and post a complete code example ? Have you checked that your problem is not already solved in the other threads titled "Cannot fit normalization function to enzyme" ? You can find a few of these threads by googling this error message. Best, Pierre On Tue, Jan 21, 2014 at 7:34 PM, Z. Ding wrote: > Hi, > > I got this “Cannot fit normalization function to enzyme, because there are > no (finite) data points in argument 'y'.” error from doCRMAv2, for 2 SNP6 > files, out of 150+ samples. A colleague run the same set of SNP6 CEL files > which caused this error without any problem, He used the same latest version > R as I did, on same/similar servers. > > Have you seem this error? It would be a great help if you can tell me what > might had caused it. Especially, how to resolve it! > > Thanks! > > Z. > > > -- > -- > 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/groups/opt_out. -- -- 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/groups/opt_out.
Re: [aroma.affymetrix] Basic manual
Hi, You can start by the website of the Aroma project: http://www.aroma-project.org/ In particular, see the "get started" tab on the left. Pierre On Thu, Jan 16, 2014 at 2:20 PM, Fernando Andrade wrote: > Hello, this is my first time using aroma.affymetrix, and I'm having many > troubles. Is there a manual covering the basics about aroma? Like > explaining which analyses can be done and the files nedded for each of them. > > 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/groups/opt_out. > -- -- 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/groups/opt_out.
Re: [aroma.affymetrix] smoothing after CRMAv2 and before CBS?
Hi Emilie, OK, so you are referring to the “smooth.CNA" function in the DNAcopy package, cf http://www.bioconductor.org/packages/2.13/bioc/vignettes/DNAcopy/inst/doc/DNAcopy.pdf What this function is doing is detecting outliers (based on how far their signal value is from their neighbors) and shrink their signal values toward those of their neighbors. This is indeed appropriate and recommended. I thought that by "smoothing" you meant performing some kind of local averaging of the original signal (e.g. using a mobile median or by binning): this I don't recommend. Sorry for the confusion. To drop outliers, one possibility is to use the "dropSegmentationOutliers" function from the PSCBS package. See the vignettes at http://cran.fhcrc.org/web/packages/PSCBS/index.html Another comment: since you are following the vignette for paired CNA analysis, I am guessing that you are working with tumor/normal pairs. If so, then you should use PSCBS rather than CBS for segmentation. PSCBS is an extension of CBS to segment not only total copy numbers but also allelic ratios. See the PSCBS vignette in the above URL. Best, Pierre On Wed, Dec 4, 2013 at 5:29 PM, Emilie wrote: > Hi Pierre, > > Thanks for your answer. I may be wrong but I thought smoothing prior to > segmentation was somewhat common. It is shown in the vignettes for DNACopy > and seems to be fairly common in the literature (this approach was used in > the Metabric paper for example, > http://www.ncbi.nlm.nih.gov/pubmed/22522925). > > I'd be interested in hearing more of your thoughts against this. Do you > have an idea of how much resolution is lost by smoothing? > > Emilie > > > > On Tuesday, December 3, 2013 5:26:38 PM UTC-5, Pierre Neuvial wrote: > >> Hi Emilie, >> >> It's certainly possible to do this within the Aroma framework (e.g. using >> the function "binnedSmoothing"). It's probably not as straightforward as >> running the segmentation directly, though, because this is not a typical >> use case. >> >> In fact, I'm not sure why you want to perform smoothing before >> segmentation ? Smoothing is definitely not required before segmentation, >> and I would actually discourage to go this path because it will end up in a >> loss of resolution along the genome at the smoothing step. >> >> Best, >> >> Pierre >> >> >> On Tue, Dec 3, 2013 at 8:53 PM, Emilie wrote: >> >>> Hi there, >>> >>> I'm new to processing Affy SNP6 chips and so am mainly experimenting >>> with different methods to date. I ran CRMAv2 and followed steps 1-4 from >>> the vignette (http://aroma-project.org/vignettes/CRMAv2). For step 5, I >>> want to do a paired analysis. >>> >>> Previously I've used DNAcopy to perform CBS for other array types, and >>> would like to follow a similar procedure, which includes smoothing prior to >>> segmentation. Is this possible using the aroma.affymetrix package? So far >>> I've followed the vignette for paired CNA analysis ( >>> http://aroma-project.org/vignettes/pairedTotalCopyNumberAnalysis) but >>> haven't seen any options for smoothing. >>> >>> thank you very much, >>> >>> emilie >>> >>> -- >>> -- >>> 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/groups/opt_out. >>> >> >> -- > -- > 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 we
Re: [aroma.affymetrix] smoothing after CRMAv2 and before CBS?
Hi Emilie, It's certainly possible to do this within the Aroma framework (e.g. using the function "binnedSmoothing"). It's probably not as straightforward as running the segmentation directly, though, because this is not a typical use case. In fact, I'm not sure why you want to perform smoothing before segmentation ? Smoothing is definitely not required before segmentation, and I would actually discourage to go this path because it will end up in a loss of resolution along the genome at the smoothing step. Best, Pierre On Tue, Dec 3, 2013 at 8:53 PM, Emilie wrote: > Hi there, > > I'm new to processing Affy SNP6 chips and so am mainly experimenting with > different methods to date. I ran CRMAv2 and followed steps 1-4 from the > vignette (http://aroma-project.org/vignettes/CRMAv2). For step 5, I want > to do a paired analysis. > > Previously I've used DNAcopy to perform CBS for other array types, and > would like to follow a similar procedure, which includes smoothing prior to > segmentation. Is this possible using the aroma.affymetrix package? So far > I've followed the vignette for paired CNA analysis ( > http://aroma-project.org/vignettes/pairedTotalCopyNumberAnalysis) but > haven't seen any options for smoothing. > > thank you very much, > > emilie > > -- > -- > 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/groups/opt_out. > -- -- 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/groups/opt_out.
Re: [aroma.affymetrix] Re: Setting up annotation data in aroma.affymetrix
>
>>> at #01.
>>> Arguments$getReadablePath("AromaAnalysis/ChipType/HG-U133_Plus_2",
>>> mustExist = TRUE)
>>> - Arguments$getReadablePath() is local of the calling function
>>>
>>> Error: Pathname not found: AromaAnalysis/ChipType/HG-U133_Plus_2 (none of
>>> the parent directories [AromaAnalysis/ChipType/] exist; current directory is
>>> 'C:/Users/nawin/AromaAnalysis/ChipType/HG-U133_Plus_2')
>>> In addition: Warning messages:
>>> 1: In is.na(parent) :
>>> is.na() applied to non-(list or vector) of type 'NULL'
>>> 2: In is.na(parent) :
>>> is.na() applied to non-(list or vector) of type 'NULL'
>>> > getwd()
>>> [1] "C:/Users/nawin/AromaAnalysis/ChipType/HG-U133_Plus_2"
>>> >
>>>
>>>
>>> I don't know why that happen
>>>
>>> On Tuesday, April 30, 2013 5:02:48 PM UTC+1, Henrik Bengtsson wrote:
>>>>
>>>> Hi.
>>>>
>>>> On Tue, Apr 30, 2013 at 8:26 AM, nawin MOHAMMED
>>>> wrote:
>>>> > hi Pierre,
>>>> >
>>>> > the anootationData is allocated by default in the aroma.affymetrix ??
>>>> > is it
>>>> > ??? as its declare in the page of aroma :
>>>> >
>>>> > Aroma.affymetrix searches for CDF files in the annotationData/
>>>> > directory of
>>>> > the current working directory. Place the CDF for chip type
>>>> > in a
>>>> > directory of format:
>>>> >
>>>> > annotationData/chipTypes//
>>>> >
>>>> >
>>>> > and my location is
>>>> >
>>>> >
>>>> > "C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/chipType/HG-U133_Plus_2
>>>> >
>>>> > i just creat new folder in annotation data with name chip type and
>>>> > inside
>>>> > it another folder with chip name ???
>>>> > iam just confused ??
>>>>
>>>> What you're missing in "Aroma.affymetrix searches for CDF files in the
>>>> annotationData/ directory of the current working directory" is the
>>>> part that says ***of the current working directory***. In other
>>>> words, in your current working directory (i.e. getwd()) you should see
>>>> subdirectory "annotationData" if you call list.files(). You may find
>>>> the following page useful too:
>>>>
>>>> http://aroma-project.org/troubleshooting/DirectoryStructures
>>>>
>>>>
>>>>
>>>> Also, I strongly recommend to put your data files (annotationData/,
>>>> rawData/, etc.) somewhere else than where R installs packages. Right
>>>> now you seem to place them in:
>>>>
>>>>
>>>> C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/chipType/HG-U133_Plus_2
>>>>
>>>> The directory 'C:/Users/nwayyin/Documents/R/win-library/3.0/' is where
>>>> R install packages and you shouldn't add/remove things from there.
>>>> For instance, if you uninstall aroma.affymetrix then all your data may
>>>> disappear as well. Instead, let your working directory be something
>>>> like:
>>>>
>>>> C:/Users/nwayyin/AromaAnalysis/
>>>>
>>>> and let that be your working directory in R.
>>>>
>>>> /Henrik
>>>>
>>>> > why this error occur please if you know the cause of problem
>>>> > please
>>>> > tell me
>>>> >
>>>> >
>>>> > On Tuesday, April 30, 2013 3:16:00 PM UTC+1, Pierre Neuvial wrote:
>>>> >>
>>>> >> Hi,
>>>> >>
>>>> >> Quoting myself,
>>>> >>
>>>> >> "1. Read carefully the setup page:
>>>> >> http://www.aroma-project.org/setup,
>>>> >> and follow the links in that page."
>>>> >>
>>>> >> The first link "Location of annotation data files" explains where
>>>> >> annotation data files should be located.
>>>> >>
>>>> >> Best,
>>>> >>
>>>> >> Pierre
>>>> >>
>>>> >>
>
Re: [aroma.affymetrix] Re: Setting up annotation data in aroma.affymetrix
Hi,
Quoting myself,
"1. Read carefully the setup page: http://www.aroma-project.org/setup,
and follow the links in that page."
The first link "Location of annotation data files" explains where
annotation data files should be located.
Best,
Pierre
On Tue, Apr 30, 2013 at 2:10 PM, nawin MOHAMMED wrote:
>
> i also down load the CDF from affymetrix but its not working same
> problem
>
> Error: Failed to create AffymetrixCdfFile object. Could not locate an
> annotation data file for chip type 'HG-U133_Plus_2' with tags 'full' and
> with filename extension 'cdf'.
>> cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2",tags="full")
> [2013-04-30 13:08:07] Exception: Failed to create AffymetrixCdfFile object.
> Could not locate an annotation data file for chip type 'HG-U133_Plus_2' with
> tags 'full' 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$byChipType("HG-U133_Plus_2", tags = "full")
> - AffymetrixCdfFile$byChipType() is local of the calling function
>
> Error: Failed to create AffymetrixCdfFile object. Could not locate an
> annotation data file for chip type 'HG-U133_Plus_2' with tags 'full' and
> with filename extension 'cdf'.
>> getwd()
> [1]
> "C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/chipType/CD_hgu133a2_libraryfile"
>>
>
>
> On Tuesday, April 30, 2013 8:40:35 AM UTC+1, Pierre Neuvial wrote:
>>
>> Hi,
>>
>> Please create a new thread (with a relevant subject line) instead of
>> replying to an unrelated one.
>>
>> See below.
>>
>> On Tue, Apr 30, 2013 at 9:22 AM, nawin MOHAMMED wrote:
>> >
>> >
>> > Greeting ,
>> >
>> > iam a Phd student , i try implement aroma package but its not working
>> > with
>> > me , i don't know where is the error, and i have question the
>> > shiptype
>> > folder is not exist be default in annotationdata, i just create a
>> > folder in annotation data name it chiptype and i put the cdf file in it
>> > , is
>> > that possible ??? please i need your advice this is my program
>> >
>> >
>> >
>>
>> Yes, that's what you should do. Here is some general advice that
>> could save you lots of time:
>>
>> 1. Read carefully the setup page: http://www.aroma-project.org/setup,
>> and follow the links in that page.
>>
>> 2. Be really careful with the folder and file names: "annotationData"
>> is not the same as "annotationdata", etc. The same holds for function
>> names in the code you have pasted below, for example
>> "AffymetrixcdfFile" is not the same as "AffymetrixCdfFile", etc...
>>
>> 3. Do not try to guess/invent code lines if you are not familiar with
>> the aroma framework. Instead, try to reproduce a vignette, for
>> example this one:
>> http://www.aroma-project.org/vignettes/GeneSTArrayAnalysis
>>
>> Best,
>>
>> Pierre
>>
>> >> getwd()
>> > [1]
>> >
>> > "C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/ChipType"
>> >> ChipType(""HG-U133_Plus_2")
>> > Error: unexpected symbol in "ChipType(""HG"
>> >> ChipType("HG-U133_Plus_2")
>> > Error: could not find function "ChipType"
>> >> chipType("HG-U133_Plus_2")
>> > Error: could not find function "chipType"
>> >> library(aroma.affymetrix)
>> >> ChipeType("HG-U133_Plus_2")
>> > Error: could not find function "ChipeType"
>> >> chipType<-"HG-U133_Plus_2"
>> >> cdf<-AffymetrixcdfFile$byChipType("HG-U133_Plus_2")
>> > Error: object 'AffymetrixcdfFile' not found
>> >> cdf<-AffymetrixcdfFile$bychipType("HG-U133_Plus_2")
>> > Error: object 'AffymetrixcdfFile' not found
>> >> cdf<-AffymetrixcdfFile$byChipType("HG-U133_Plus_2")
>> > Error: object 'AffymetrixcdfFile' not found
>> >> cdf<-HG-U
[aroma.affymetrix] Setting up annotation data in aroma.affymetrix
Hi,
Please create a new thread (with a relevant subject line) instead of
replying to an unrelated one.
See below.
On Tue, Apr 30, 2013 at 9:22 AM, nawin MOHAMMED wrote:
>
>
> Greeting ,
>
> iam a Phd student , i try implement aroma package but its not working with
> me , i don't know where is the error, and i have question the shiptype
> folder is not exist be default in annotationdata, i just create a
> folder in annotation data name it chiptype and i put the cdf file in it , is
> that possible ??? please i need your advice this is my program
>
>
>
Yes, that's what you should do. Here is some general advice that
could save you lots of time:
1. Read carefully the setup page: http://www.aroma-project.org/setup,
and follow the links in that page.
2. Be really careful with the folder and file names: "annotationData"
is not the same as "annotationdata", etc. The same holds for function
names in the code you have pasted below, for example
"AffymetrixcdfFile" is not the same as "AffymetrixCdfFile", etc...
3. Do not try to guess/invent code lines if you are not familiar with
the aroma framework. Instead, try to reproduce a vignette, for
example this one:
http://www.aroma-project.org/vignettes/GeneSTArrayAnalysis
Best,
Pierre
>> getwd()
> [1]
> "C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/ChipType"
>> ChipType(""HG-U133_Plus_2")
> Error: unexpected symbol in "ChipType(""HG"
>> ChipType("HG-U133_Plus_2")
> Error: could not find function "ChipType"
>> chipType("HG-U133_Plus_2")
> Error: could not find function "chipType"
>> library(aroma.affymetrix)
>> ChipeType("HG-U133_Plus_2")
> Error: could not find function "ChipeType"
>> chipType<-"HG-U133_Plus_2"
>> cdf<-AffymetrixcdfFile$byChipType("HG-U133_Plus_2")
> Error: object 'AffymetrixcdfFile' not found
>> cdf<-AffymetrixcdfFile$bychipType("HG-U133_Plus_2")
> Error: object 'AffymetrixcdfFile' not found
>> cdf<-AffymetrixcdfFile$byChipType("HG-U133_Plus_2")
> Error: object 'AffymetrixcdfFile' not found
>> cdf<-HG-U133_Plus_2$bychipType("HG-U133_Plus_2")
> Error: object 'HG' not found
>> cdf<-AffymetrixcdfFile$bychipType("HG-U133_Plus_2", tags=ChipType)
> Error: object 'AffymetrixcdfFile' not found
>>
>
> the error is with cdf file which can not be read
> i download all the package
>
> source("http://bioconductor.org/biocLite.R";)
>
> biocLite("biomaRt")
>
> hbInstall("aroma.affymetrix")
>
> thank you
>
--
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Re: [aroma.affymetrix] Errors when processed Vignette:CRMAv2
Hi,
This thread should help you solving your problem:
https://groups.google.com/forum/?fromgroups=#!topic/aroma-affymetrix/S_wLLGcU8S0
Cheers,
Pierre
On Fri, Jan 4, 2013 at 6:58 PM, Foxchase wrote:
> Dear Henrik,
> I'm trying aroma.affymetrix for Affy's Affymetrix Mouse Diversity Genotyping
> Array. I made the arom annotation files using Affy's na32's NetAffx files.
> I use a public data 'GSE27691". Attached is the R history file.
> When I followed the Vignette:CRMAv2 I got error at the step:> cesN <-
> process(fln, verbose=verbose):
>
>> cesN <- process(fln, verbose=verbose)
> 20130104 12:05:43|Normalizing set for PCR fragment-length effects...
> 20130104 12:05:44| Identifying SNP and CN units...
> types
> 1 2 5
>24 626135 1832538
> 20130104 12:05:44| subsetToUpdate:
>int [1:2458673] 25 26 27 28 29 30 31 32 33 34 ...
> 20130104 12:05:44| Identifying SNP and CN units...done
> 20130104 12:05:44| Retrieving SNP information annotations...
> UflSnpInformation:
> Name: MOUSEDIVm520650
> Tags:
> Full name: MOUSEDIVm520650
> Pathname: annotationData/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650.ufl
> File size: 9.38 MB (9834930 bytes)
> RAM: 18.76 MB
> Chip type: MOUSEDIVm520650
> Number of enzymes: 2
> 20130104 12:05:44| Retrieving SNP information annotations...done
> 20130104 12:05:44| Identifying the subset used to fit normalization
> function(s)...
>int [1:2292403] 25 26 27 28 29 30 31 32 33 34 ...
> 20130104 12:05:44| Identifying the subset used to fit normalization
> function(s)...done
> 20130104 12:05:44| Shift: 0
> 20130104 12:05:44| onMissing: median
> 20130104 12:05:44| Array #1 of 7 ('GSM685813')...
> 20130104 12:05:44| Reading and filtering fragment lengths...
> 20130104 12:05:44| Reading fragment lengths...
> UflSnpInformation:
> Name: MOUSEDIVm520650
> Tags:
> Full name: MOUSEDIVm520650
> Pathname: annotationData/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650.ufl
> File size: 9.38 MB (9834930 bytes)
> RAM: 18.76 MB
> Chip type: MOUSEDIVm520650
> Number of enzymes: 2
> 20130104 12:05:46|Summary of non-filtered fragment lengths:
> int [1:2458673, 1:2] 2744 2744 2744 2744 2744 2744 572 572 572 572 ...
>V1 V2
> Min. :7Min. :7
> 1st Qu.: 6161st Qu.: 542
> Median : 1149Median : 999
> Mean : 1623Mean : 1478
> 3rd Qu.: 21983rd Qu.: 2002
> Max. :32767Max. :32767
> NA's :233634 NA's :233634
> 20130104 12:05:46| Reading fragment lengths...done
> 20130104 12:05:46| Filtering fragment lengths...
> 20130104 12:05:46| Filtering fragment lengths...done
> 20130104 12:05:46| Reading and filtering fragment lengths...done
> V1 V2
>Min. :7Min. :7
>1st Qu.: 6161st Qu.: 542
>Median : 1149Median : 999
>Mean : 1623Mean : 1478
>3rd Qu.: 21983rd Qu.: 2002
>Max. :32767Max. :32767
>NA's :233634 NA's :233634
>int [1:2292403] 1 2 3 4 5 6 7 8 9 10 ...
> UflSnpInformation:
> Name: MOUSEDIVm520650
> Tags:
> Full name: MOUSEDIVm520650
> Pathname: annotationData/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650.ufl
> File size: 9.38 MB (9834930 bytes)
> RAM: 18.76 MB
> Chip type: MOUSEDIVm520650
> Number of enzymes: 2
> 20130104 12:05:47| Setting up predefined target functions...
> 20130104 12:05:47| Target type: zero
> 20130104 12:05:47| Setting up predefined target functions...done
> 20130104 12:05:47| Getting cell matrix map...
> 'UnitGroupCellMatrixMap' int [1:2458673, 1] 25 26 27 28 29 30 31 32 33
> 34 ...
> 20130104 12:05:48| Getting cell matrix map...done
> 20130104 12:05:48| Getting theta estimates...
> 20130104 12:05:49| Thetas:
> num [1:2458673, 1] 1047 477 3533 3499 3353 ...
> num [1:2458673, 1] 1047 477 3533 3499 3353 ...
> V1
> Min. : -143
> 1st Qu.: 1785
> Median : 4562
> Mean : 6687
> 3rd Qu.: 9142
> Max. :199787
> 20130104 12:05:49| Getting theta estimates...done
> 20130104 12:05:49| Calculating total signals...
> 20130104 12:05:49| Total thetas:
> num [1:2458673] 1047 477 3533 3499 3353 ...
> 20130104 12:05:49| Calculating total signals...done
> 20130104 12:05:49| Normalizing log2 signals...
> 20130104 12:05:49| Log2 signals:
> num [1:2458673] 10 8.9 11.8 11.8 11.7 ...
> [2013-01-04 12:05:50] Exception: Cannot fit normalization function, because
> none of the units are on fragments from a single enzyme, or equivalently,
> there exist no rows in argument 'fragmentLenghts' that only have one finite
> value.
> at #04. normalizeFragmentLength.default(y, fragmentLengths = fl,
> targetFcns = targetFcns,
> subsetToFit = subset, onMissing = onMissing, ...)
> - normalizeFragmentLength.default() is in environment
> 'aroma.light'
> at #03. normalizeFragmentLength(y, fragmentLengths = f
Re: [aroma.affymetrix] Help with SNP6 normalization
Hi Joshy,
In order to narrow down the problem it would be nice to have some
information about the output of your script.
First, can you add an 'str' instruction in your last loop, as below:
for( chr in 1:24)
{
units <- getUnitsOnChromosome(gi,chromosome=chr);
pos <- getPositions(gi,units = units)
unitNames <- getUnitNames(cdf,units = units)
theta <- extractMatrix(cesN,units = units)
#theta <- extractMatrix(ces,units = units)
str(theta)
rownames(theta) <- unitNames
all.data <- rbind(all.data,theta)
}
and paste the R output in your reply?
Cheers,
Pierre
On Sat, Sep 15, 2012 at 9:51 PM, joshy wrote:
> Hi
> I have used the attached R script to normalize a bunch of SNP6 CEL files
> before. Recently I updated the aroama.affymetrix package and the output of
> the script does not make sense. Can anyone help me.
>
> Jg
>
> --
> 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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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 in "getGenomeInformation"
Hi,
The error message says: "Failed to retrieve genome information for
this chip type: GenomeWideSNP_6"
>From your reply to my message in your other thread "Problem with
AffymetrixCelSet cmd" it looks like you are indeed missing annotation
files. (Currently you only have the cdf, which basically connects
each location on the microarray to the corresponding probe idea; but
you don't have any information on the location of the probes on the
genome, which is why you get the above error message.)
Try to follow the CRMAv2 vignette:
http://aroma-project.org/vignettes/CRMAv2 step by step. In the
"Setup" section of that vignette you will find how to get the other
annotation files. And then your analysis should work properly.
Note that the 'doCRMAv2' block is essentially a wrapper that executes
the preprocessing step described in more detail in the above vignette.
Cheers,
Pierre
On Mon, Jun 18, 2012 at 10:58 PM, NT_CMU wrote:
> Hi
>
> I'm trying to run the command "doCRMAv2", and i get these errors. Let me
> know what the problem is, if any of you have encountered this before. I
> thought i did not have some library installed but, i have both ACNE and
> aroma.affymetrix working properly.
>
>> ds <- doCRMAv2("LeeAV_2012",chipType="GenomeWideSNP_6,Full")
> Error in getGenomeInformation.AffymetrixCdfFile(cdf) :
> [2012-06-18 16:55:10] Exception: Failed to retrieve genome information for
> this chip type: GenomeWideSNP_6
>
> at #12. getGenomeInformation.AffymetrixCdfFile(cdf)
> - getGenomeInformation.AffymetrixCdfFile() is in environment
> 'aroma.affymetrix'
>
> at #11. getGenomeInformation(cdf)
> - getGenomeInformation() is in environment 'aroma.affymetrix'
>
> at #10. getSubsetToAvg.AllelicCrosstalkCalibration(this)
> - getSubsetToAvg.AllelicCrosstalkCalibration() is in environment
> 'aroma.affymetrix'
>
> at #09. getSubsetToAvg(this)
> - getSubsetToAvg() is in environment 'aroma.affymetrix'
>
> at #08. getParameters.AllelicCrosstalkCalibration(this)
> - getParameters.AllelicCrosstalkCalibration() is in environment
> 'aroma.affymetrix'
>
> at #07. getParameters(this)
> - getParameters() is in environment 'R.rsp'
>
> at #06. process.AllelicCrosstalkCalibration(acc, verbose = verbose)
> - process.AllelicCrosstalkCalibration() is in environment
>
>
> Thanks
>
> Nitesh
>
> --
> 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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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] Problem with AffymetrixCelSet cmd
Hi,
On Mon, Jun 18, 2012 at 5:39 PM, NT_CMU wrote:
> Hi
>
> I am new to aroma.affymetrix. I am not sure why the command
> "AffymetrixCelSet$byName" is not working.
>
> cs <- AffymetrixCelSet$byName("test.CEL",chipType =
> "../../annotationData/chipTypes/GenomeWideSNP_6")
This will not work because
1- the first argument of 'AffymetrixCelSet$byName' should be the name
of your data set (this is why this function is called "byName"), as it
appears in your "rawData" folder. Is should not be a file name as
"test.CEL"
2- the 'chipType' argument should really be a chip type, e.g.
"GenomeWideSNP_6", not a path to a cdf file (as
"../../annotationData/chipTypes/GenomeWideSNP_6" is).
More below.
> Error in method(static, ...) :
> [2012-06-18 11:34:57] Exception: Failed to create AffymetrixCdfFile object.
> Could to locate an annotation data file for chip type
> '../../annotationData/chipTypes/GenomeWideSNP_6' (without requiring any
> tags) and with filename extension 'cdf'.
>
> at #04. method(static, ...)
> - method() is in environment 'aroma.core'
>
> at #03. AffymetrixCdfFile$byChipType(chipType)
> - AffymetrixCdfFile$byChipType() is local of the calling function
>
> at #02. method(static, ...)
> - method() is in environment 'aroma.affymetrix'
>
> at #01. AffymetrixCelSet$byName("test.CEL", chipType =
> "../../annotationData/chipTypes/GenomeWideSNP_6")
> - AffymetrixCelSet$byName() is local of the calling function
>
>
> I think my directory structure is wrong. But i could use some pointers on
> how to get things moving because i've been trying to get this command
> working for over 4 days now.
I don't know what your file structure is, can you describe it ?
Your file structure should match this one:
http://aroma-project.org/setup/QuickSummaryOfRequiredFileStructure
When you have that, you should be able to define an AffymetrixCelSet using
"AffymetrixCelSet$byName", for example
cs <- AffymetrixCelSet$byName("myDataSet",chipType="GenomeWideSNP_6")
where "myDataSet" is a character string containing the name of your
data set (not file names), and "GenomeWideSNP_6" is your chip type.
Important note: you should make sure that the working directory of
your R session contains "annotationData", "rawData", etc.
Is that the case for you ?
Cheers,
Pierre
PS (quoting Henrik): "If you find yourself specifying paths or full
pathname in your main
aroma.affymetrix scripts, you are doing something wrong. The package
is design to work without having to specify paths. A rule of thumb is
that you should be able to move any aroma.affymetrix script to another
computer system and run it without having to change anything." [thread
'How do you analyze Gene ST Data?', Oct 21, 2008].
>
> Also, another issue is I am able to load CDF files with the basic
> "AffymetrixCdfFile("GenomeWideSNP_6,Full.CDF") ". But if i use the command
> AffymetrixCdfFile$byChipType("GenomeWideSNP_6",tags="Full"), it gives me an
> error. Am I doing something really wrong?
>
> Thanks
>
> Nitesh
>
>
> --
> 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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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 when Creating binary data files containing copy number estimates (Agilent HG-CGH-244A)
Hi,
On Wed, May 16, 2012 at 9:05 PM, sean nj wrote:
>
> Hi,
>
> I did get rid of the error message when I ran :
>
> > unf <- TextUnitNamesFile$byChipType(chipType)
>
> I got this done by loading the aroma.affymetrix package, in addition to
> aroma.core.
>
> But now I got another error message when I followed Henrik's code at
> http://aroma-project.org/node/88
>
> I was trying to creating data files containing log2 CN ratios. Everything was
> fine until I ran
>
> > units <- indexOf(unf, unitNames)
> Error in indexOf.UnitNamesFile(unf, unitNames) :
> [2012-05-16 14:53:18] Exception: If specified, argument 'pattern' must be a
> single string. Did you mean to use argument 'names'?
> at #02. indexOf.UnitNamesFile(unf, unitNames)
> - indexOf.UnitNamesFile() is in environment 'aroma.core'
> at #01. indexOf(unf, unitNames)
> - indexOf() is in environment 'R.filesets'
> >
>
>From the error message (pretty explicit) it looks like you should have done
units <- indexOf(unf, names=unitNames)
instead of
units <- indexOf(unf, unitNames)
That's what you do below.
Cheers,
Pierre
> The command ran successfully when I tried to get units for certain probes
>
> > units <- indexOf(unf, names=c("A_16_P15025341","A_16_P00013121")
> + )
> > units
> [1] 1006 1019
> >
> I tried > ?indexOf.UnitNamesFile() and here is what I got:
>
> indexOf(this, pattern=NULL, names=NULL, ...)
>
> Arguments
>
> pattern A pattern to be used for identifying unit names of interest. If
> NULL, no regular expression matching is done.
>
>
>
> names Names to be match exactly to the unit names.
>
> ... Not used.
>
>
> What did I do wrong?
>
> Thanks a lot for the help!
>
> Ying
>
> > sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252 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.affymetrix_2.5.0 affxparser_1.28.0 aroma.apd_0.2.2
> R.huge_0.3.0
> [5] aroma.core_2.5.0 aroma.light_1.24.0 matrixStats_0.5.0
> R.rsp_0.7.5
> [9] R.filesets_1.1.5 digest_0.5.2 R.cache_0.6.2
> R.utils_1.12.1
> [13] R.oo_1.9.3 R.methodsS3_1.2.2
> loaded via a namespace (and not attached):
> [1] tools_2.15.0
> >
>
>
> On Tue, May 15, 2012 at 12:38 PM, sean nj wrote:
>>
>> Hi guys,
>>
>> I was following the Vignette: Creating binary data files containing copy
>> number estimates and trying to work on agilent HG-CGH-244A chip. I
>> downloaded and unzipped the .gz of the
>> HG-CGH-244A,TCGA,HB20080512,unitNames.txt and
>> HG-CGH-244A,TCGA,HB20080512.ugp and put them in
>> H:\Aroma_Analysis\annotationData\chipTypes\HG-CGH-244A folder. Then I tried
>> to run the same code on the vignette and got the error right away (please
>> see end of this email). Did I do something wrong?
>>
>> I have one more question regarding "Creating data files containing log2 CN
>> ratios" with HG-CGH-244A chip. The data I have are level 2 files from TCGA.
>> There is one txt file for each sample (not the original .asb file) and its
>> format is like:
>>
>>
>> Hybridization REF MSK_1_251469322729_S01_CGH-v4_91
>>
>> Composite Element REF normalizedLog2Ratio
>>
>> A_14_P112718 0.135431541355747
>>
>> A_16_P15000916 0.441719513563848
>>
>> A_16_P15001074 0.227252175271962
>>
>> A_16_P0012 0.231158251618718
>>
>> A_16_P0014 -0.0623833233443793
>>
>> .
>>
>> ..
>>
>> My first question is, does this kind data file work?
>>
>> My second question is, do I need to create a folder rawCnData as mentioned
>> in the vignette (Pathname:
>> rawCnData/MyDataSet,tagA,tagB/HG-CGH-244A/SampleA,tagA,tagB,log2ratio,total.asb)?
>> I also have the rawData folder which holds affy snp6 and expression data.
>>
>>
>>
>> Thanks a lot for the help!
>>
>>
>>
>> Ying
>>
>> > library(aroma.core)
>> > chipType <- "HG-CGH-244A"
>> > unf <- TextUnitNamesFile$byChipType(chipType)
>> Error in method(static, ...) :
>> [2012-05-15 12:12:26] Exception: Failed to create TextUnitNamesFile object.
>> Could to locate an annotation data file for chip type 'HG-CGH-244A' (without
>> requiring any tags) and with filename extension 'names' (this may not be the
>> correct extension as it was guessed from the class name 'TextUnitNamesFile').
>>
>> at #02. method(static, ...)
>> - method() is in environment 'aroma.core'
>> at #01. TextUnitNamesFile$byChipType(chipType)
>> - TextUnitNamesFile$byChipType() is local of the calling function
>> > sessionInfo()
>> R version 2.15.0 (2012-03-30)
>> Platform: x86_64-pc-mingw32/x64 (64-
Re: [aroma.affymetrix] [aroma.affymetrix] Error when converting CustomCDF to binary format!
Hi Ying,
This is a question for the Bioconductor mailing list, because it had
to do with the affxparser package (and nothing to do with the aroma
framework). Can you post it there ?
Cheers,
Pierre
On Mon, May 7, 2012 at 10:07 PM, sean nj wrote:
> Hi guys,
>
> I tried to convert recent customCDF HTHGU133A_Hs_ENTREZG.cdf (version 15.10)
> to binary format and end up with error message:
>
> Error in convertCdf("HTHGU133A_Hs_ENTREZG.cdf",
> "HTHGU133A_Hs_ENTREZG,Binary.cdf", :
> An inconsistency between source and destination CDF was detected.
> Reason:Units:
> Any suggestion?
>
> Thanks,
>
> Ying
>
>> library(affxparser)
>> convertCdf("HTHGU133A_Hs_ENTREZG.cdf","HTHGU133A_Hs_ENTREZG,Binary.cdf",
> + version = 4,force = TRUE,verbose=TRUE)
> Reading CDF header...
> Reading CDF header...done
> Reading CDF QC units...
> Reading CDF QC units...done
> Reading CDF units...
> Reading CDF units...done
> Writing CDF structure...
> Timing for writeCdf():
> user system elapsed
> 10.11 0.02 10.14
> Writing CDF structure...done
> Comparing CDFs...
> Comparing CDFs...
> CDF 1: ./HTHGU133A_Hs_ENTREZG.cdf
> CDF 2: ./HTHGU133A_Hs_ENTREZG,Binary.cdf
> Comparing CDF headers...
> Comparing CDF headers...done
> Comparing QC units...
> Comparing QC units...done
> Comparing units...
> Error in convertCdf("HTHGU133A_Hs_ENTREZG.cdf",
> "HTHGU133A_Hs_ENTREZG,Binary.cdf", :
> An inconsistency between source and destination CDF was detected.
> Reason:Units:
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> States.1252
> [3] LC_MONETARY=English_United States.1252
> 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] affxparser_1.28.0 BiocInstaller_1.4.4
> loaded via a namespace (and not attached):
> [1] tools_2.15.0
>>
>
>
> --
> 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/
--
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] Paired CBS
Hi Michelle, Yes: just replace plotTracks(fit); by plotTracks(fit, chromosome=2); Best, Pierre On Mon, May 7, 2012 at 11:48 PM, Michelle wrote: > Hi Henrik, > > On this page http://aroma-project.org/vignettes/PairedPSCBS-lowlevel you > showed how to make whole genome plots of TCN, the > decrease-of-heterozygosity (DH), and the minor-major CN estimates. Is there > a way to make such plots for individual chromosomes? > > Thanks, > Michelle > > > > On Fri, Feb 17, 2012 at 6:04 PM, Henrik Bengtsson > wrote: >> >> Hi, >> >> On Fri, Feb 17, 2012 at 1:44 PM, Michelle wrote: >> > Hi Henrik, >> > >> > I ran the PSCBS package on some Affy SNP 6.0 arrays. In the output I >> > found >> > that several files contain a few lines of negative "tcnMean" values, >> > while >> > the rest are all positive. My question is - the total copy number is >> > supposed to be positive, right? Are these negative values caused by some >> > error in the computation? If so, how to adjust them? >> >> yes, *true*/*biological* CNs cannot be negative. However, >> *observed*/*estimated* ones may very well end up being *slightly* >> negative, due to noise in data. So, it is neither a bug nor something >> wrong with PSCBS. >> >> There is nothing in Paired PSCBS that enforces the CNs to be strictly >> non-negative (>= 0), neither does it restrict the CN estimates to be >> integers (0, 1, 2, 3, ...), because there may be normal cell >> contamination or tumor clonality. However, you can imagine that there >> are downstream methods that takes the PSCBS estimates and make such >> decisions, but that is not part of PSCBS itself. >> >> You can always manual adjust negative estimates to be zero, if you >> really need them not to be negative, but I still haven't had to do it. >> >> /Henrik >> >> > >> > Thanks, >> > Michelle >> > >> > -- >> > 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/ >> >> -- >> 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/ > > > -- > 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/ -- 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/
Re: [aroma.affymetrix] Error in Paired PSCBS with CytoScanHD
Hi,
On Wed, Apr 18, 2012 at 3:05 PM, Sathish Periyasamy <
sathish.periyas...@gmail.com> wrote:
> I am getting the following error segs <- getSegments(fit); The error
> output is as follows:
>
> Please assist me in solving the following error.
>
> regards
>
>chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs
> tcnNbrOfHets
>1 25 11 1598 16148 26 1.955 26
> 1
> dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean
>11598 16148 1 0.3252 0.6596 1.295 chromosome tcnId dhId
> tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets
>1 25 11 1598 16148 26 1.955 26
> 1
> dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean
>11598 16148 1 0.3252 0.6596 1.295 chromosome tcnId dhId
> tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets
>1 25 11 1598 16148 26 1.955 26
> 1
> dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean
>11598 16148 1 0.3252 0.6596 1.295 chromosome tcnId dhId
> tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets
>1 25 11 1598 16148 26 1.955 26
> 1
> dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean
>11598 16148 1 0.3252 0.6596 1.29520120418 15:49:56|
> Chromosome #25 ('Chr25') of 25...done20120418 15:49:56| Merging
> (independently) segmented chromosome...Error: cannot allocate vector of size
> 17.3 Mb
>
>
The first error is actually here (just above).
17.3 Mb is really not much, and should not be a problem. Maybe you have
large objects in your R session. Can you try again from a fresh R session ?
Another possibility is that you have other programs than R taking all your
RAM.
More below.
> In addition: There were 50 or more warnings (use warnings() to see the first
> 50)20120418 15:50:43| Merging (independently) segmented
> chromosome...done20120418 15:50:43| Segmenting multiple
> chromosomes...done20120418 15:50:43|Segmenting paired tumor-normal signals
> using Paired PSCBS...done> > segs <- getSegments(fit);Error in
> UseMethod("getSegments") :
> no applicable method for 'getSegments' applied to an object of class
> "function"
>
>
Your 'fit' object was not created because of the above error, hence this
second error ('fit' is also a function in your R environment).
Cheers,
Pierre
> #segs <- getSegments(fit);> print(segs);Error in print(segs) : object 'segs'
> not found> #help("segmentByPairedPSCBS", package="PSCBS");> > pairName <-
> paste(pair, collapse="vs");> chrTag <- sprintf("Chr%s",
> seqToHumanReadable(getChromosomes(fit)));Error in UseMethod("getChromosomes")
> :
> no applicable method for 'getChromosomes' applied to an object of class
> "function"> > toPNG(pairName, tags=c(chrTag, "PairedPSCBS"), width=840,
> aspectRatio=0.6, {+ plotTracks(fit);+ });Error in paste(c(name, tags),
> collapse = ",") : object 'chrTag' not found
>
> >
>
> --
> 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/
>
--
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] object 'cns' not found
Hi Andy,
On Mon, Apr 16, 2012 at 4:15 AM, Andyusa wrote:
> HI All,
>
> It was my first time to use the aroma to run two pairs of samples vs
> controls, but it turn out failure (detail below). Could anyone give me some
> advices? Thanks. Andy
>
> library("aroma.affymetrix");
> verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
> # Don't display too many decimals.
> options(digits=4);
>
> Preprocessing using CRMAv2
>
> dataSet <- "cancerpairs";
> chipType <- "GenomeWideSNP_6";
> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full");
> dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE, verbose=verbose);
> dsC <- dsList$total;
> print(dsC);
>> print(dsC);
> AromaUnitTotalCnBinarySet:
> Name: cancerpairs
> Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
> Full name: cancerpairs,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
> Number of files: 4
> Names: 11-0368_SNP_6-0, 11-0428_SNP_6-0, 11-5141_SNP_6-0, 11-5209_SNP_6-0
> [4]
> Path (to the first file):
> totalAndFracBData/cancerpairs,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY/GenomeWideSNP_6
> Total file size: 28.71 MB
> RAM: 0.01MB
>
>
>
> idxT <- match(c("11-0428_SNP_6-0.CEL","11-0368_SNP_6-0.CEL"),getNames(dsC));
>> dsT <- extract(dsC, idxT);
> Warning messages:
> 1: In min(x) : no non-missing arguments to min; returning Inf
> 2: In max(x) : no non-missing arguments to max; returning -Inf
>>
This warning suggests that idxT is empty, ie the samples you were
trying to match were not found.
Can you check ?
The reason for this is (at least) that 'getNames' does not return the
extension (e.g. ".CEL") of the files. 'getFullNames' would do that,
but it's better to stick with 'getNames' and remove the ".CEL" of the
character strings you are trying to match.
>> idxN <- match(c("11-5209_SNP_6-0.CEL","11-5141_SNP_6-0.CEL"),
>> getNames(dsC));
>> dsN <- extract(dsC, idxN);
> Warning messages:
> 1: In min(x) : no non-missing arguments to min; returning Inf
> 2: In max(x) : no non-missing arguments to max; returning -Inf
Same here.
As a consequence, dsN and dsT are NA, and the instruction below gives an error.
Pierre
>> cns <- CbsModel(dsT, dsN);
> Error in file(pathname, open = "rb") : cannot open the connection
> In addition: Warning message:
> In file(pathname, open = "rb") :
> cannot open file 'NA': No such file or directory
>> print(cns);
> Error in print(cns) : object 'cns' not found
>
>
> sessionInfo()
> R version 2.14.2 (2012-02-29)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915
> [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] DNAcopy_1.28.0 preprocessCore_1.16.0 sfit_0.2.0
> [4] calmate_0.9.2 MASS_7.3-17 aroma.affymetrix_2.5.0
> [7] affxparser_1.26.4 aroma.apd_0.2.2 R.huge_0.3.0
> [10] aroma.core_2.5.0 aroma.light_1.22.0 matrixStats_0.4.4
> [13] R.rsp_0.7.5 R.cache_0.6.2 R.filesets_1.1.5
> [16] digest_0.5.2 R.utils_1.12.1 R.oo_1.9.3
> [19] R.methodsS3_1.2.2
>
> loaded via a namespace (and not attached):
> [1] splines_2.14.2
>>
>
>
> traceback()
> 1: print(cns)
>
> --
> 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/
--
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] Re: ACNE getGenomeInformation(cdf) failed
Hi,
On Thu, Apr 5, 2012 at 10:17 AM, Frederic Foucault
wrote:
> Hello,
>
> I follow the setup of the vignette but failed again
>
> setwd("c:/Users/foucault/Bioinformatic/acne/Test/")
>> library("aroma.affymetrix");
>> library("ACNE");
>> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>>
>> dataSet <- "GSE14996,testSet";
>
>> chipType <- "GenomeWideSNP_6";
>> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full");
>> print(cdf);
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/GenomeWideSNP_6
> Filename: GenomeWideSNP_6,Full.cdf
> Filesize: 470.44MB
> Chip type: GenomeWideSNP_6,Full
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2572x2680
> Number of cells: 6892960
> Number of units: 1881415
> Cells per unit: 3.66
> Number of QC units: 4
>
>> gi <- getGenomeInformation(cdf);
> Error in getGenomeInformation.AffymetrixCdfFile(cdf) :
> [2012-04-05 10:12:33] Exception: Failed to retrieve genome information for
> this chip type: GenomeWideSNP_6
>
>
> at #02. getGenomeInformation.AffymetrixCdfFile(cdf)
> - getGenomeInformation.AffymetrixCdfFile() is in environment
> 'aroma.affymetrix'
>
> at #01. getGenomeInformation(cdf)
> - getGenomeInformation() is in environment 'aroma.affymetrix'
>
> Thank you for your help,
> Frederic
>
>
Did you place all the annotation files in the
annotationData/chipTypes/GenomeWideSNP_6 folder ?
It looks that this one is missing :
"GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp"
Do these file appear in the output of
path <- getPath(cdf)
list.files(path)
If not, then add them and retry.
If yes then I'm missing something.
Cheers,
Pierre
Pierre
>
>
> Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit :
>>
>> Hello,
>>
>> I want to get allele specific copy number from SNP6 CL files
>> I´m following the vignette for ACNE.
>> I installed the annotation data in \test\annotationData\chipTypes
>> \GenomeWideSNP6.0
>>
>> "GenomeWideSNP_6,Full,HB20080710.acs"
>> "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl"
>> "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp"
>> "GenomeWideSNP_6,Full.cdf"
>>
>> GenomeWideSNP_6,Full.cdf is from Affymetrix while the three others are
>> from aroma
>>
>> here is the error :
>> gi <- getGenomeInformation(cdf);
>> Error in getGenomeInformation.AffymetrixCdfFile(cdf) :
>> [2012-04-04 16:48:48] Exception: Failed to retrieve genome information
>> for this chip type: GenomeWideSNP_6
>>
>> at #02. getGenomeInformation.AffymetrixCdfFile(cdf)
>> - getGenomeInformation.AffymetrixCdfFile() is in environment
>> 'aroma.affymetrix'
>>
>> at #01. getGenomeInformation(cdf)
>> - getGenomeInformation() is in environment
>> 'aroma.affymetrix'
>>
>>
>> Thank you for your help
>> Frederic
>>
>
> Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit :
>>
>> Hello,
>>
>> I want to get allele specific copy number from SNP6 CL files
>> I´m following the vignette for ACNE.
>> I installed the annotation data in \test\annotationData\chipTypes
>> \GenomeWideSNP6.0
>>
>> "GenomeWideSNP_6,Full,HB20080710.acs"
>> "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl"
>> "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp"
>> "GenomeWideSNP_6,Full.cdf"
>>
>> GenomeWideSNP_6,Full.cdf is from Affymetrix while the three others are
>> from aroma
>>
>> here is the error :
>> gi <- getGenomeInformation(cdf);
>> Error in getGenomeInformation.AffymetrixCdfFile(cdf) :
>> [2012-04-04 16:48:48] Exception: Failed to retrieve genome information
>> for this chip type: GenomeWideSNP_6
>>
>> at #02. getGenomeInformation.AffymetrixCdfFile(cdf)
>> - getGenomeInformation.AffymetrixCdfFile() is in environment
>> 'aroma.affymetrix'
>>
>> at #01. getGenomeInformation(cdf)
>> - getGenomeInformation() is in environment
>> 'aroma.affymetrix'
>>
>>
>> Thank you for your help
>> Frederic
>>
>
> Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit :
>>
>> Hello,
>>
>> I want to get allele specific copy number from SNP6 CL files
>> I´m following the vignette for ACNE.
>> I installed the annotation data in \test\annotationData\chipTypes
>> \GenomeWideSNP6.0
>>
>> "GenomeWideSNP_6,Full,HB20080710.acs"
>> "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl"
>> "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp"
>> "GenomeWideSNP_6,Full.cdf"
>>
>> GenomeWideSNP_6,Full.cdf is from Affymetrix while the three others are
>> from aroma
>>
>> here is the error :
>> gi <- getGenomeInformation(cdf);
>> Error in getGenomeInformation.AffymetrixCdfFile(cdf) :
>> [2012-04-04 16:48:48] Exception: Failed to retrieve genome information
>> for this chip type: GenomeWideSNP_6
>>
>> at #02. getGenomeInformation.AffymetrixCdfFile(cdf)
>> - getGenomeInformation.AffymetrixCdfFile() is in environment
>> 'aroma.affymetrix'
>>
>> at #01. getGenomeInformation(cdf)
>> - getGenomeInformation() is in environment
>> 'aroma.affymetrix'
>>
>>
>> Thank you for your help
>> Frederic
>>
>
> Le mercredi 4 avr
[aroma.affymetrix] Processing multiple Affymetrix arrays
(forgot to cc the list)
-- Forwarded message --
From: Pierre Neuvial
Date: Wed, Nov 16, 2011 at 10:16 PM
Subject: Re: [aroma.affymetrix] Processing multiple Affymetrix arrays
To: Anguraj Sadanandam
Hi Anguraj,
On Wed, Nov 16, 2011 at 4:13 PM, Anguraj Sadanandam
wrote:
>
> Hi Henrik,
>
> I am interested in processing about 228 Affy SNP 6.0 array samples. I used
> the following code (attached below). Though it was working well, I was trying
> to get the raw data through a loop (as you can see in the code below). I was
> executing the loop for 228 times for that many samples (may be not a good
> idea). The code stopped somewhere around 162. This happened 2 times but not
> exactly at 162. May be the loop is not the best way. Could you please suggest
> the better way? I like to increase the number of samples up to 1070 and is it
> good idea to do it by batch or do it all together? I have the normal samples
> for normalization.
>
> My sessioninfo() is below.
>
> Thanks,
>
> Anguraj
>
>
>
> dataSet <- "Panc";
> chipType <- "GenomeWideSNP_6,Full";
> expNbrOfArrays <- 228;
>
>
> library("aroma.affymetrix");
> verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
>
> cdf <- AffymetrixCdfFile$byChipType(chipType);
> print(cdf);
>
> # Assert that all annotation data files exist
> gi <- getGenomeInformation(cdf);
> print(gi);
>
> si <- getSnpInformation(cdf);
> print(si);
>
> acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE));
> print(acs);
>
> # Setup data set
> cs <- AffymetrixCelSet$byName(dataSet, cdf=cdf);
> print(cs);
> # Sanity check
> stopifnot(nbrOfArrays(cs) == expNbrOfArrays);
>
>
> # Step 1: Crosstalk calibration
> acc <- AllelicCrosstalkCalibration(cs);
> print(acc);
> csC <- process(acc, verbose=verbose);
> print(csC);
>
>
> # Step 2 - Normalization for nucleotide-position probe sequence effects
> bpn <- BasePositionNormalization(csC, target="zero");
> print(bpn);
> csN <- process(bpn, verbose=verbose);
> print(csN);
>
>
> # Step 3 - Probe summarization
> plm <- AvgCnPlm(csN, mergeStrands=TRUE, combineAlleles=TRUE);
> print(plm);
>
> if (length(findUnitsTodo(plm)) > 0) {
> # Fit CN probes quickly (~5-10s/array + some overhead)
> units <- fitCnProbes(plm, verbose=verbose);
> str(units);
> # int [1:945826] 935590 935591 935592 935593 935594 935595 ...
> # Fit remaining units, i.e. SNPs (~5-10min/array)
> units <- fit(plm, verbose=verbose);
> str(units);
> }
>
> # Get the estimated chip effects
> ces <- getChipEffectSet(plm);
> print(ces);
>
>
> # Step 4 - Normalization for PCR fragment-length effects
> fln <- FragmentLengthNormalization(ces);
> print(fln);
> cesN <- process(fln, verbose=verbose);
> print(cesN);
>
FYI, you could replace Step 1 through 4 by
cesN <- doCRMAv2(cs)
see http://www.aroma-project.org/blocks/doCRMAv2
>
> # Sanity check
> stopifnot(nbrOfArrays(cesN) == expNbrOfArrays);
>
> # Identify the index of all normal samples by mapping to names in a text
> file (
> or whatever you wish)
> normalNames <- readLines("normal.txt");
> #normals <- indexOf(cesN, normalNames);
> normals <- match(normalNames, getNames(cesN))
> str(normals);
> stopifnot(all(is.finite(normals))); # Sanity check
>
> # Extract pool of reference samples (normals only)
> cesR <- extract(cesN, normals);
> print(cesR);
>
> # Calculate the robust average across this pool
> ceR <- getAverageFile(cesR, verbose=verbose);
> print(ceR);
>
> #cesR <- cesNHapMap;
> #print(cesR);
> ceR <- getAverageFile(cesR, verbose=verbose);
> print(ceR);
>
> # Set up the CBS model with ceR as the reference for all samples
> cbs <- CbsModel(cesN, ceR);
> print(cbs);
>
> # Fit the segmentation
> #fit(cbs, verbose=verbose);
>
> gi <- getGenomeInformation(cdf)
> print(gi)
>
> l<-NULL
> for(i in 1:23) {
> units <- getUnitsOnChromosome(gi, chromosome=i);
> pos <- getPositions(gi, units=units);
> l[i]<-length(pos)
> }
>
> length(l)
>
> l_sum<-sum(l)
>
> raw<-NULL
>
> for(i in 1:228) {
> cat("\n",i,"\n")
> for(j in 1:23) {
> rawCNs <- extractRawCopyNumbers(cbs, array=i, chromosome=j)
> raw<-rbind(raw,as.data.frame(rawCNs))
> cat(j,"\n")
> }
> }
>
Here you are trying to concatenate copy number estimates for all
samples in a huge data.frame.
Remember that the SNP 6 array has roughly 2 million loci ! After 162
iterations, this data.frame has about 324 m
Re: [aroma.affymetrix] accessing chip effect sets
Hi wisekh6,
Although you don't give the code you used to process this data, from
what you report it looks like you initially processed your data set
using the "full" chip type. See below.
On Fri, Nov 11, 2011 at 7:22 AM, wisekh6 wrote:
> Dear all,
>
> After processing Affymetrix GenomeWide SNP 6.0, I wanted to access
> 'chip effect data set' by using:
> cesN <- CnChipEffectSet$byName("AffyTestData",tags="ACC,ra,-XY,BPN,-
> XY,AVG,FLN,-XY", chipType="GenomeWideSNP_6")
>
> But, it failed, generating an error message: can't locate...
Here you try to retrieve the data set as if it had been processed
using the standard (ie non "full") chip type, and apparently it was
not the case.
>
> Using the following command successfully worked:
> cesN <- CnChipEffectSet$byName("AffyTestData",tags="ACC,ra,-XY,BPN,-
> XY,AVG,FLN,-XY", chipType="GenomeWideSNP_6,Full")
>
This one works because what you ask to retrieve corresponds to what
you did initially.
> The only difference is that the latter command used
> "GenomeWideSNP_6,Full" as chipType rather than "GenomeWideSNP_6."
>
> Does anyone let me know why the former command failed to work?
> Originally, I believed that the former command would be correct.
As explained above, both commands are "correct", but the first one
cannot retrieve what you ask because the corresponding processed data
set does not exist.
>
> FYI: The corresponding annotation file is in the following directory:
> annotationData\chipTypes\GenomeWideSNP_6
>
>
> Thank you.
>
I hope this helps,
Pierre
>
> --
> 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/
>
--
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] core dump error after upgrading R
What is your sessionInfo() ?
Perhaps you need to upgrade aroma.affymetrix instead, although I don't
see why you would get this core dump.
Pierre
On Mon, Nov 7, 2011 at 6:20 PM, Peter Kang wrote:
> I just upgraded to 2.14.0 (Mac OSX), and I'm getting a 'core dumped'
> error when trying to access the cdf file.
>
>> cdf <- AffymetrixCdfFile$byChipType("Mapping250K_Nsp")
>> print(cdf)
> zsh: abort (core dumped) R
>
> Do I need to downgrade R?
>
> Thank you.
>
> --
> 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/
>
--
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] Problem with doCRMAv2
Hi Ivan,
On Tue, Oct 25, 2011 at 1:35 AM, Ivan Smirnov wrote:
> Hi Henrik,
>
> I am trying to run the script:
>
> options(echo = FALSE,digits=4)
> library(aroma.affymetrix)
> verbose <- Verbose(threshold=-8, timestamp=TRUE);
> dataSet="Gupta_CC"
> chipType <- "GenomeWideSNP_6"
> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full");
> print(cdf)
> dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE, verbose=verbose);
> dsC <- dsList$total;
> print(dsC);
>
>
> and it is crushing with:
>
> 20111024 16:05:12| Normalizing set for PCR fragment-length effects...
> 20111024 16:05:12| Identifying SNP and CN units...
> types
> 1 2 5
> 621 934968 945826
> 20111024 16:05:13| subsetToUpdate:
> int [1:1880794] 622 623 624 625 626 627 628 629 630 631 ...
> 20111024 16:05:13| Identifying SNP and CN units...done
> 20111024 16:05:13| Retrieving SNP information annotations...
> 20111024 16:05:13| Defining DChipSnpInformation from chip type...
> 20111024 16:05:13| Chip type: GenomeWideSNP_6
> 20111024 16:05:13| Version:
> 20111024 16:05:13| Located pathname:
> 20111024 16:05:13| Defining DChipSnpInformation from chip type...done
Do you have UGP and UFL annotation files in your
annotationData/chipTypes/GenomeWideSNP_6 ? From the above error it
looks like
instead you have (very) old SNP annotation files, which are not used
anymore within the Aroma Project, cf
http://www.mail-archive.com/aroma-affymetrix@googlegroups.com/msg01456.html
If you don't have UGP and UFL annotation files, please download them from
http://www.aroma-project.org/chipTypes/GenomeWideSNP_6
Hope this helps,
Pierre.
> Error in list(`doCRMAv2(dataSet, cdf = cdf, combineAlleles = FALSE,
> verbose = verbose)` = , :
>
> [2011-10-24 16:05:13] Exception: Failed to retrieve SNP information
> for this chip type: GenomeWideSNP_6
> at throw(Exception(...))
> at throw.default("Failed to retrieve SNP information for this chip type: ",
> ch
> at throw("Failed to retrieve SNP information for this chip type: ", chipType)
> at getSnpInformation.AffymetrixCdfFile(cdf)
> at getSnpInformation(cdf)
> at process.FragmentLengthNormalization(fln, verbose = verbose)
> at process(fln, verbose = verbose)
> at doCRMAv2.AffymetrixCelSet(csR, ..., verbose = verbose)
> at doCRMAv2(csR, ..., verbose = verbose)
> at doCRMAv2.character(dataSet, cdf = cdf, combineAlleles = FALSE, verbose =
> ve
> at doCRMAv2(dataSet, cdf = cdf, combineAlleles = FALSE, verbose = verbose)
> Calls: doCRMAv2 ... getSnpInformation.AffymetrixCdfFile -> throw ->
> throw.default -> throw -> throw.Exception
> 20111024 16:05:13| Retrieving SNP information annotations...done
> 20111024 16:05:13| Normalizing set for PCR fragment-length effects...done
> Execution halted
>
>
> So, it seems to have problem getting info from CDF file. But
> print(cdf) looks normal:
>
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/GenomeWideSNP_6
> Filename: GenomeWideSNP_6,Full.cdf
> Filesize: 470.44MB
> Chip type: GenomeWideSNP_6,Full
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2572x2680
> Number of cells: 6892960
> Number of units: 1881415
> Cells per unit: 3.66
> Number of QC units: 4
>
> and the check sum is identical to one posted on the web:
> "3fbe0f6e7c8a346105238a3f3d10d4ec"
>
> All my software is up to date. Any clues?
>
> Thanks
> Ivan
>
> --
> 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/
>
--
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] warnings and error message in reading affy snp6.0 cel file
Hi Qian,
I'm not sure what the warnings mean, but please see below for the error.
On Mon, Oct 17, 2011 at 4:19 PM, Qian wrote:
>
> Dear all,
> I just start learning aroma.affymetrix package for Affy SNP6.0
> analysis. I downloaded ugp,ufl,acs file from the link
> http://www.aroma-project.org/chipTypes/GenomeWideSNP_6, followed the
> example code, but I got the following warnings. I can't move to the
> following steps. Would you please let me know what the problem is?
>
> Thanks a lot,
> Qian
> > cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6",tags="Full");
> > print(cdf);
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/GenomeWideSNP_6
> Filename: GenomeWideSNP_6,Full.cdf
> Filesize: 470.44MB
> Chip type: GenomeWideSNP_6,Full
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2572x2680
> Number of cells: 6892960
> Number of units: 1881415
> Cells per unit: 3.66
> Number of QC units: 4
>
> > gi <- getGenomeInformation(cdf)
> Warning messages:
> 1: In readBin(con = con, what = integer(), size = 4, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> 2: In readBin(con = con, what = integer(), size = 4, n = n, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> 3: In readBin(con = con, what = integer(), size = 4, n = n, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> 4: In readBin(con = con, what = integer(), size = 4, n = n, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> 5: In readBin(con = con, what = integer(), size = 4, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> 6: In readBin(con = con, what = integer(), size = 4, n = n, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> 7: In readBin(con = con, what = integer(), size = 4, n = n, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> 8: In readBin(con = con, what = integer(), size = 4, n = n, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> > print(gi);
> UgpGenomeInformation:
> Name: GenomeWideSNP_6
> Tags: Full,na31,hg19,HB20110328
> Full name: GenomeWideSNP_6,Full,na31,hg19,HB20110328
> Pathname: annotationData/chipTypes/GenomeWideSNP_6/
> GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp
> File size: 8.97 MB (9407867 bytes)
> RAM: 0.00 MB
> Chip type: GenomeWideSNP_6,Full
> Warning messages:
> 1: In readBin(con = con, what = integer(), size = 4, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> 2: In readBin(con = con, what = integer(), size = 4, n = n, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> 3: In readBin(con = con, what = integer(), size = 4, n = n, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> 4: In readBin(con = con, what = integer(), size = 4, n = n, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> 5: In readBin(con = con, what = integer(), size = 4, n = n, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> > si <- getSnpInformation(cdf)
> Warning messages:
> 1: In readBin(con = con, what = integer(), size = 4, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> 2: In readBin(con = con, what = integer(), size = 4, n = n, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> 3: In readBin(con = con, what = integer(), size = 4, n = n, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> 4: In readBin(con = con, what = integer(), size = 4, n = n, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> > print(si)
> UflSnpInformation:
> Name: GenomeWideSNP_6
> Tags: Full,na31,hg19,HB20110328
> Full name: GenomeWideSNP_6,Full,na31,hg19,HB20110328
> Pathname: annotationData/chipTypes/GenomeWideSNP_6/
> GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl
> File size: 7.18 MB (7526452 bytes)
> RAM: 0.00 MB
> Chip type: GenomeWideSNP_6,Full
> Number of enzymes: 2
> Warning messages:
> 1: In readBin(con = con, what = integer(), size = 4, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> 2: In readBin(con = con, what = integer(), size = 4, n = n, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> 3: In readBin(con = con, what = integer(), size = 4, n = n, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> 4: In readBin(con = con, what = integer(), size = 4, n = n, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> 5: In readBin(con = con, what = integer(), size = 4, n = n, signed =
> FALSE, :
> 'signed = FALSE' is only valid for integers of sizes 1 and 2
> > acs <- AromaCellSequenceF
Re: [aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file
Hi,
Have you tried using extractAffyBatch, which is documented here:
http://aroma-project.org/howtos/extractAffyBatch ?
As far as I understand you will need the Bioconductor annotation
package corresponding to your chip type to be installed, ie
source("http://www.bioconductor.org/biocLite.R";)
biocLite("hgu133plus2cdf")
This is discussed in this thread:
http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/40e3950e52d73c1f/772e387a3163db56
Pierre
On Tue, Aug 9, 2011 at 4:34 AM, hsingjun cheung
wrote:
> Hi Pierre:
>
> Thanks. These functions work now. Do you know how to extract the raw
> intensity for each probe ?
>
> On Aug 8, 5:48 pm, Pierre Neuvial wrote:
>> Hi,
>>
>> The 'annotationData' directory should be directly in your working
>> directory, as explained in the page "Setup: Location of annotation
>> data files":http://aroma-project.org/node/66
>>
>> In your case, you need to change the current directory to ~/experiment/ by
>>
>> setwd("~/experiment/")
>>
>> (or by starting your R session from this directory). Then your command
>>
>> csR <- AffymetrixCelSet$byName("KN01M013",chipType="HG-U133_Plus_2")
>>
>> should work.
>>
>> Best,
>>
>> Pierre
>>
>> On Mon, Aug 8, 2011 at 5:29 PM, hsingjun cheung
>>
>>
>>
>>
>>
>>
>>
>> wrote:
>> > Hello:
>>
>> > I searched the group but got no results ... So I want to know, how to
>> > extract the raw probe intensity from .CEL file?
>>
>> > The file structure on my computer is like:
>>
>> > ~/experiemnt/
>> > annotationData/
>> > chipTypes/
>> > HG-U133_Plus_2/
>> > HG-U133_Plus_2.cdf
>> > ~/experiment/
>> > rawData/
>> > KN01M013/
>> > HG-U133_Plus_2/
>> > KN01M013.CEL
>>
>> > The .cdf file is downloaded
>> > fromhttp://www.aroma-project.org/chipTypes/HG-U133_Plus_2
>>
>> > When I run R under ~ directory:
>> > library(aroma.affymetrix)
>> > csR <- AffymetrixCelSet$byName("KN01M013",chipType="HG-U133_Plus_2")
>>
>> > I got error msg:
>>
>> > Error in list(`AffymetrixCelSet$byName("KN01M013", chipType = "HG-
>> > U133_Plus_2")` = , :
>>
>> > [2011-08-08 11:24:05] Exception: Could not locate a file for this chip
>> > type: HG-U133_Plus_2
>> > at throw(Exception(...))
>> > at throw.default("Could not locate a file for this chip type: ",
>> > paste(c(chipT
>> > at throw("Could not locate a file for this chip type: ",
>> > paste(c(chipType, tag
>> > at method(static, ...)
>> > at AffymetrixCdfFile$byChipType(chipType)
>> > at method(static, ...)
>> > at AffymetrixCelSet$byName("KN01M013", chipType = "HG-U133_Plus_2")
>>
>> > Could anyone help me figure how this error happened ? And how to do
>> > it ( extract raw probe intensity ) in a right way ? 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 websitehttp://www.aroma-project.org/.
>> > To post to this group, send email to aroma-affymetrix@googlegroups.com
>> > To unsubscribe and other options, go tohttp://www.aroma-project.org/forum/
>
> --
> 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/
>
--
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/
Re: [aroma.affymetrix] How to extract raw probe intensity from .CEL file
Hi,
The 'annotationData' directory should be directly in your working
directory, as explained in the page "Setup: Location of annotation
data files":
http://aroma-project.org/node/66
In your case, you need to change the current directory to ~/experiment/ by
setwd("~/experiment/")
(or by starting your R session from this directory). Then your command
csR <- AffymetrixCelSet$byName("KN01M013",chipType="HG-U133_Plus_2")
should work.
Best,
Pierre
On Mon, Aug 8, 2011 at 5:29 PM, hsingjun cheung
wrote:
> Hello:
>
> I searched the group but got no results ... So I want to know, how to
> extract the raw probe intensity from .CEL file?
>
> The file structure on my computer is like:
>
> ~/experiemnt/
> annotationData/
> chipTypes/
> HG-U133_Plus_2/
> HG-U133_Plus_2.cdf
> ~/experiment/
> rawData/
> KN01M013/
> HG-U133_Plus_2/
> KN01M013.CEL
>
> The .cdf file is downloaded from
> http://www.aroma-project.org/chipTypes/HG-U133_Plus_2
>
> When I run R under ~ directory:
> library(aroma.affymetrix)
> csR <- AffymetrixCelSet$byName("KN01M013",chipType="HG-U133_Plus_2")
>
> I got error msg:
>
> Error in list(`AffymetrixCelSet$byName("KN01M013", chipType = "HG-
> U133_Plus_2")` = , :
>
> [2011-08-08 11:24:05] Exception: Could not locate a file for this chip
> type: HG-U133_Plus_2
> at throw(Exception(...))
> at throw.default("Could not locate a file for this chip type: ",
> paste(c(chipT
> at throw("Could not locate a file for this chip type: ",
> paste(c(chipType, tag
> at method(static, ...)
> at AffymetrixCdfFile$byChipType(chipType)
> at method(static, ...)
> at AffymetrixCelSet$byName("KN01M013", chipType = "HG-U133_Plus_2")
>
>
>
> Could anyone help me figure how this error happened ? And how to do
> it ( extract raw probe intensity ) in a right way ? Thanks
>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
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Re: [aroma.affymetrix] aroma.affymetrix can't read cdf file
Hi Yaping,
The cdf file should not be in the working directory, but in a
chip-type-specific subdirectory of the 'annotationData' directory, as
explained in the page "Setup: Location of annotation data files":
http://aroma-project.org/node/66
Please see this page for further info. In your example, the cdf file
should be in
annotationData/chipTypes/Mapping250K_Nsp
Best,
Pierre
On Thu, Aug 4, 2011 at 11:20 PM, Yaping Feng wrote:
> hi,
> I just installed aroma.affymetrix in my mac computer (Mac OS X 10.6.7). The
> R version is 2.13.1.
> I want to read this cdf file "Mapping250K_Nsp.cdf":
>
> cdf <- AffymetrixCdfFile$byChipType("Mapping250K_Nsp")
>
> Error in list(`AffymetrixCdfFile$byChipType("Mapping250K_Nsp")` =
> , :
>
> [2011-08-04 16:01:17] Exception: Could not locate a file for this chip type:
> Mapping250K_Nsp
> at throw(Exception(...))
> at throw.default("Could not locate a file for this chip type: ",
> paste(c(chipType, tags), collapse = ","))
> at throw("Could not locate a file for this chip type: ", paste(c(chipType,
> tags), collapse = ","))
> at method(static, ...)
> at AffymetrixCdfFile$byChipType("Mapping250K_Nsp")
>
>
> The cdf file is in the current directory. Can anybody tell me how to fix it!
> Thanks,
> Yaping
>
> --
> 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/
>
--
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] Aroma Affymetrix shell variable path?
Hi Fong,
The standard way to do this within the Aroma framework is to use
*links* to the directories you need. The best way to do this depends
on your OS, but in general this can be done within R using the
function 'createLink' (from R.utils), e.g.:
createLink(target="~/Data/annotationData")
createLink(target="~/Data/rawData")
will create in the working directory a link to "~/Data/annotationData"
called "annotationData", and a link to "~/Data/rawData" called
"rawData".
In general I think that it is very sound to separate the actual
location of the data from the location of your scripts, and that's
exactly what you can do with links.
Note that if you'd like the results of your analyses to be written in
your usual data directory ("~/Data" in the above example) instead of
your current working directory, then you will also have to do
something like
createLink(target="~/Data/probeData")
createLink(target="~/Data/plmData")
Hope this helps,
Pierre
On Mon, Mar 14, 2011 at 7:09 PM, Fong wrote:
> Hi,
>
> Is there a way to use aroma affymetrix code without having to be in
> the aroma affymetrix directory? When I am outside of the aroma
> affymetrix directory and I try to enter the command:
>
>> cdf <- AffymetrixCdfFile$byChipType('HG-U133_Plus_2', tags='ense')
> Error in list(`AffymetrixCdfFile$byChipType("HG-U133_Plus_2", tags =
> "ense")` = , :
>
> [2011-03-14 10:56:12] Exception: Could not locate a file for this chip
> type: HG-U133_Plus_2,ense
> at throw(Exception(...))
> at throw.default("Could not locate a file for this chip type: ",
> paste(c(chipT
> at throw("Could not locate a file for this chip type: ",
> paste(c(chipType, tag
> at method(static, ...)
> at AffymetrixCdfFile$byChipType("HG-U133_Plus_2", tags = "ense")
>>
>
> All this code is in a R script and the easy solution would be to set
> the directory to that be the aroma affymetrix directory using
> setwd(). But I was wondering if there was some aroma affymetrix shell
> variable I could set so that it knows where to look for the aroma
> affymetrix files without having to explicitly set the directory. I
> haven't been able to find any references to this in the forums.
>
> Thanks,
>
> Fong
>
> --
> 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/
>
--
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/
Re: [aroma.affymetrix] fracB and BAF values
Hi Allab, 'fracB' in the Aroma world has the same meaning as 'BAF' in the Illumina BeadStudio world, that is, as you say, the fraction of signal coming from the B allele at a given SNP: yB/(yA+yB). So the short answer is that there is no conversion needed from 'fracB' to 'BAF'. [Side note: we decided to call it 'fracB' instead of BAF because we believe that the term 'frequency' is misleading as it suggests a calculation across a population of samples.] More details: In BeadStudio the BAF signals are truncated at 0 and 1, which is why you only observe values in this range. On the other hand, aroma.affymetrix implements (AS)-CRMAv2, in which signals are *not* truncated, mainly because such a truncation results in a loss of information. In particular, truncation introduces non-linearities in the signals, which is not always (and IMHO, generally not) a good idea. If you want values between 0 and 1, you can still truncate them afterwards. Even more details: the main reason why there are values out of the range in the first place is that raw intensity values are corrected for offset and allelic crosstalk (see the CRMA v1 and CRMA v2 papers in http://aroma-project.org/publications). Note that a similar type of correction is performed by BeadStudio, but truncation hides the values outside of [0,1]. Does this answer your question ? Best, Pierre On Mon, Dec 20, 2010 at 5:51 PM, allab wrote: > Dear aroma users/authors, > i am doing now Affy 6.0 SNP data analysis and my goal is to become BAF > values (B-allele frequency) as they were output from Illumina > software. > BAF is a normalized metric which reflects the proportion of B-alleles > in each SNP, e.g. 0 for AA SNP, 0.5 for an AB SNP and 1 for BB. > I have generated fracB values with aroma package and see now that > there are also negative values for fracB, but as i understand it > correctly BAF values should be in the range between 0 and 1. > The question is, how can i convert fracB values into BAF values. > 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 > "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/ > -- 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/
Re: [aroma.affymetrix] DNA segmentation result
Hi,
Sure, it will be quicker.
In this case, you only have to setup the CBS segmentation model, and
fit it. For example:
## define the segmentation model
## (and its parameters)
seg <- CbsModel(ds, min.width=5);
## perform the segmentation
## (possibly for a subset of arrays and chromosomes)
fit(seg, array=2, chromosome=5, verbose=TRUE);
There are other examples on the aroma project website, e.g.
http://aroma-project.org/vignettes/pairedTotalCopyNumberAnalysis
Best,
Pierre
On Mon, Nov 29, 2010 at 7:33 PM, Yan Jiao wrote:
> Hi,
>
> Sorry to bother you again
>
> If I don't need the chromosome Explorer as result, I just need that excel
> file with copy number in (regions.xls, in CBS folder), how should I set the
> parameter, I guess it will speed up the procedure as well, right?
>
> Many thanks
>
> yan
>
> -Original Message-
> From: aroma-affymetrix@googlegroups.com
> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
> Sent: 28 November 2010 22:57
> To: aroma-affymetrix
> Subject: Re: [aroma.affymetrix] DNAcopy parameter
>
> On Sun, Nov 28, 2010 at 6:01 AM, Pierre Neuvial
> wrote:
>> Hi,
>>
>> The parameters used are the default parameters of the 'segment'
>> function of the DNAcopy package. If you search for 'DNAcopy
>> parameters' on the "Search forum" box at http://aroma-project.org, you
>> will find this recent thread which gives an example of how these
>> parameters can be changed:
>>
>> http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/aa9db6ac7835d828/b6ab6b1c9786d9ff
>
> Note that I just posted a follow up on that thread clarified that it
> is now possible to specify optional arguments specific to
> DNAcopy::segment() as:
>
> seg <- CbsModel(ds, min.width=5);
>
> In order to find out which they are and what they do, see the specific
> segmentation method, i.e. help("segment", package="DNAcopy").
>
> /Henrik
>
>>
>> Hope this helps.
>>
>> Pierre
>>
>> On Wed, Nov 24, 2010 at 7:31 PM, Yan Jiao wrote:
>>> Thanks Henrik,
>>> I will update my R and aroma package,
>>> Another question is what kind of parameters of aroma use for copy number
>>> segmentation, if using DNAcopy as the algorithm?
>>>
>>> Many thanks
>>>
>>> yan
>>>
>>> -Original Message-
>>> From: aroma-affymetrix@googlegroups.com
>>> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
>>> Sent: 24 November 2010 17:06
>>> To: aroma-affymetrix
>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>
>>> Ok, after seing your sessionInfo();
>>>
>>> You need to update to R v2.12.0, especially since you're on Windows
>>> 64-bit. Lots of work have been done by R core people to support
>>> Windows 64-bit on R v2.12.0 and beyond. There is no shortcut to this.
>>>
>>> Update aroma.affymetrix to v1.8.0, cf. http://aroma-project.org/install
>>>
>>> Also, the Cairo package is not available for the 64-bit version of R
>>> on Windows. If you try install.packages("Cairo") on your Windows
>>> machine, CRAN should report that package is not available. Either
>>> you have installed it by other means or it incorrectly installed on R
>>> v2.11.0.
>>>
>>> /Henrik
>>>
>>>
>>> On Wed, Nov 24, 2010 at 8:58 AM, Yan Jiao wrote:
>>>> Hi Henrik,
>>>>
>>>> I did what you suggested:
>>>>
>>>>> traceback()
>>>>
>>>> 13: stop(gettextf("package '%s' is not installed for 'arch=%s'",
>>>>
>>>> pkgname, r_arch), call. = FALSE, domain = NA)
>>>>
>>>> 12: testRversion(pkgInfo, package, pkgpath)
>>>>
>>>> 11: library(package, lib.loc = lib.loc, character.only = TRUE,
>>>> logical.return = TRUE,
>>>>
>>>> warn.conflicts = warn.conflicts, keep.source = keep.source)
>>>>
>>>> 10: base::require(...)
>>>>
>>>> 9: require("Cairo")
>>>>
>>>> 8: findPngDevice.default(transparent = FALSE)
>>>>
>>>> 7: findPngDevice(transparent = FALSE)
>>>>
>>>> 6: plot.CopyNumberSegmentationModel(model, path = path, imageFormat =
>>>> "png",
>>>>
>>>> plotband = plotband, arrays = arrays, ...)
>>>>
&
Re: [aroma.affymetrix] Copy number segmentation result
Hi,
On Wed, Nov 24, 2010 at 4:17 PM, Yan Jiao wrote:
> Hi Henrik,
>
> Another question about the result is : is there a way to map the copy number
> to the gene ID automatically?
You mean retrieving a list of genes contained in each DNAcopy segment
? No, this is not implemented in aroma.*
You can use (for example) the biomaRt package to do this.
> Also does aroma choose threshold for calling gain and loss?
No, aroma.* just calls the DNAcopy::segment function for you, and this
function just performs segmentation, and gives you the mean copy
number in each segment. It does not call gains or losses.
Cheers,
Pierre
>
> Many thanks
>
> yan
>
> -Original Message-
> From: aroma-affymetrix@googlegroups.com
> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
> Sent: 24 November 2010 15:08
> To: aroma-affymetrix
> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
> Hi,
>
> great. Contrary to error messages, warnings are alright to get.
>
> /H
>
> On Wed, Nov 24, 2010 at 2:51 AM, Yan Jiao wrote:
>> Thank you Henrik,
>> It works now, but I got some warning:
>>
>> process(ce, verbose=TRUE);
>> Generating ChromosomeExplorer report...
>> Loading required package: Cairo
>> Generating ChromosomeExplorer report...done
>> [1] TRUE
>> Warning messages:
>> 1: In library(package, lib.loc = lib.loc, character.only = TRUE,
>> logical.return = TRUE, :
>> there is no package called 'Cairo'
>> 2: In method(static, ...) :
>> Ghostscript not found. Searched directories: C:/gs, C:\Program Files/gs,
>> /gs, C:\Program Files\Common Files/gs
>>
>> Are those warning messages serious? Could I ignore them?
>>
>>
>> Yan
>>
>> -Original Message-
>> From: aroma-affymetrix@googlegroups.com
>> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
>> Sent: 23 November 2010 21:53
>> To: aroma-affymetrix
>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>
>> Hi.
>>
>> On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao wrote:
>>> Hi Henrik,
>>>
>>> Sorry, the error is after
>>> cbs <- CbsModel(ds);
>>> ce <- ChromosomeExplorer(cbs);
>>> process(ce, verbose=TRUE);
>>
>> Ok, now the error message makes a bit more sense (it was my suspicion
>> but I didn't want make guesses).
>>
>>>
>>>
>>> Generating ChromosomeExplorer report...
>>> Loading required package: Cairo
>>> >> to load shared library
>>> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll':
>>> LoadLibrary failure: The specified module could not be found.
>>>
>>> And there is a pop out window saying: The program can't start because
>>> libgsl-0.dll I smissing from your computer. Try reinstalling the program
>>> to fix this program.
>>
>> I can reproduce this on 64-bit Windows 7 - you get the same error if
>> you try library("GLAD"). It is because we utilize part of the GLAD
>> package, if and only if it is *installed*, and otherwise we turn to
>> backup solutions. What happens here is that *GLAD is installed but
>> doesn't load*, which causes the error so that backup solutions doesn't
>> kick in. In the next release I'll try to make sure the backup
>> solutions will also work when there is an error load GLAD. In
>> meanwhile, you can do this:
>>
>> WORKAROUND:
>>
>> 1. Uninstall the GLAD package (it doesn't work anyway):
>>
>>> remove.packages("GLAD")
>> Removing package(s) from 'C:\Users\hb\R\win-library\2.12'
>> (as 'lib' is unspecified)
>>
>>> library("GLAD")
>> Error in library("GLAD") : there is no package called 'GLAD'
>>
>> That should do it. Let me know if it works for you.
>>
>> TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL)
>> is not installed on the system (hence the 'gsl' part of
>> 'libgsl-0.dll'). There is a hard-to-find note that you need GSL in
>> order to use the GLAD package, cf.
>> http://bioconductor.org/packages/release/bioc/html/GLAD.html. There
>> exist 32-bit binaries of GSL at
>> http://gnuwin32.sourceforge.net/packages/gsl.htm. Unfortunately, it
>> does not work for the 64-bit version of R on Windows 64-bit. It works
>> if you do tricks an run the 32-bit version of R, but that is a rather
>> inconvenient workaround.
>>
>> /Henrik
>>
>>>
>>>
>>> Yan
>>>
>>> -Original Message-
>>> From: aroma-affymetrix@googlegroups.com
>>> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
>>> Sent: 23 November 2010 18:50
>>> To: aroma-affymetrix
>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>
>>> Hi.
>>>
>>> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao wrote:
Dear all,
I'm trying to do DNA segmentation,
This is what I'm doing:
ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240",
>>> verbose=TRUE);
###this is done sucessfully
# Segmentation
cbs <- CbsModel(ds);
I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm
>>> trying
to use DNAcopy for segmentation.
>>>
>>> Is it really t
Re: [aroma.affymetrix] DNAcopy parameter
Hi,
The parameters used are the default parameters of the 'segment'
function of the DNAcopy package. If you search for 'DNAcopy
parameters' on the "Search forum" box at http://aroma-project.org, you
will find this recent thread which gives an example of how these
parameters can be changed:
http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/aa9db6ac7835d828/b6ab6b1c9786d9ff
Hope this helps.
Pierre
On Wed, Nov 24, 2010 at 7:31 PM, Yan Jiao wrote:
> Thanks Henrik,
> I will update my R and aroma package,
> Another question is what kind of parameters of aroma use for copy number
> segmentation, if using DNAcopy as the algorithm?
>
> Many thanks
>
> yan
>
> -Original Message-
> From: aroma-affymetrix@googlegroups.com
> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
> Sent: 24 November 2010 17:06
> To: aroma-affymetrix
> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
> Ok, after seing your sessionInfo();
>
> You need to update to R v2.12.0, especially since you're on Windows
> 64-bit. Lots of work have been done by R core people to support
> Windows 64-bit on R v2.12.0 and beyond. There is no shortcut to this.
>
> Update aroma.affymetrix to v1.8.0, cf. http://aroma-project.org/install
>
> Also, the Cairo package is not available for the 64-bit version of R
> on Windows. If you try install.packages("Cairo") on your Windows
> machine, CRAN should report that package is not available. Either
> you have installed it by other means or it incorrectly installed on R
> v2.11.0.
>
> /Henrik
>
>
> On Wed, Nov 24, 2010 at 8:58 AM, Yan Jiao wrote:
>> Hi Henrik,
>>
>> I did what you suggested:
>>
>>> traceback()
>>
>> 13: stop(gettextf("package '%s' is not installed for 'arch=%s'",
>>
>> pkgname, r_arch), call. = FALSE, domain = NA)
>>
>> 12: testRversion(pkgInfo, package, pkgpath)
>>
>> 11: library(package, lib.loc = lib.loc, character.only = TRUE,
>> logical.return = TRUE,
>>
>> warn.conflicts = warn.conflicts, keep.source = keep.source)
>>
>> 10: base::require(...)
>>
>> 9: require("Cairo")
>>
>> 8: findPngDevice.default(transparent = FALSE)
>>
>> 7: findPngDevice(transparent = FALSE)
>>
>> 6: plot.CopyNumberSegmentationModel(model, path = path, imageFormat = "png",
>>
>> plotband = plotband, arrays = arrays, ...)
>>
>> 5: plot(model, path = path, imageFormat = "png", plotband = plotband,
>>
>> arrays = arrays, ...)
>>
>> 4: writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes =
>> chromosomes,
>>
>> zooms = zooms, ..., verbose = less(verbose))
>>
>> 3: writeGraphs(this, arrays = arrays, chromosomes = chromosomes,
>>
>> zooms = zooms, ..., verbose = less(verbose))
>>
>> 2: process.ChromosomeExplorer(ce.all, verbose = TRUE)
>>
>> 1: process(ce.all, verbose = TRUE)
>>
>>> sessionInfo()
>>
>> R version 2.11.0 (2010-04-22)
>>
>> x86_64-pc-mingw32
>>
>> locale:
>>
>> [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United
>> Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
>> LC_NUMERIC=C
>>
>> [5] LC_TIME=English_United Kingdom.1252
>>
>> attached base packages:
>>
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>>
>> [1] RColorBrewer_1.0-2 DNAcopy_1.22.1 preprocessCore_1.10.0
>> sfit_0.1.9 aroma.affymetrix_1.7.0 aroma.apd_0.1.7
>> affxparser_1.20.0
>>
>> [8] R.huge_0.2.0 aroma.core_1.7.0 aroma.light_1.16.1
>> matrixStats_0.2.2 R.rsp_0.4.0 R.cache_0.3.0
>> R.filesets_0.9.0
>>
>> [15] digest_0.4.2 R.utils_1.5.3 R.oo_1.7.4
>> R.methodsS3_1.2.1
>>
>> loaded via a namespace (and not attached):
>>
>> [1] tools_2.11.0
>>
>>>
>>
>> process(ce,chromosomes=c(1,8,17), verbose=-10)
>>
>> Generating ChromosomeExplorer report...
>>
>> Setting up ChromosomeExplorer report files...
>>
>> Copying template files...
>>
>> Source path:
>> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/includes
>>
>> Destination path: reports/includes
>>
>> Copying template files...done
>>
>> Setting up ChromosomeExplorer report files...done
>>
>> Explorer output version: 3
>>
>> Compiling ChromosomeExplorer.onLoad.js.rsp...
>>
>> Source:
>> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp
>>
>> Output path: reports/Fockens_1/ACC,-XY,RMA,+300,A+B,FLN,-XY
>>
>> Scanning directories for available chip types...
>>
>> Detected chip types: Mapping50K_Hind240
>>
>> Scanning directories for available chip types...done
>>
>> Scanning image files for available zooms...
>>
>> Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64
>>
>> Scanning image files for available zooms...done
>>
>> Scanning directory for subdirectories...
>>
>> Detected (or default) sets: cbs
>>
>> Scanning directory for subdirectories...done
>>
>> Compiling RSP...
>>
>> member data.c
Re: [aroma.affymetrix] subselect samples for segmentation
Hi Yan,
You're right: removing files manually from data folders generated by
aroma.* is not a good idea. This is can be done directly within R
using the methods provided by the package.
In your case, I think you were doing :
cbs <- CbsModel(ds);
ce <- ChromosomeExplorer(cbs);
process(ce, chromosomes=c(1,8,17), verbose=TRUE);
To run the segmentation on the first two samples, you can do
process(ce, arrays=c(1,2), chromosomes=c(1,8,17), verbose=TRUE);
If you want to specify the *names* of samples to be segmented, you can use
idxs <- indexOf(ce, sampleNames);
process(ce, arrays=idxs, chromosomes=c(1,8,17), verbose=TRUE);
where 'sampleNames' is a vector of sample names.
More generally, one can use the 'extract' method on any set of data files, e.g.
ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240", verbose=TRUE);
idxs <- indexOf(ce, sampleNames);
dsSub <- extract(ds, idxs);
Hope this helps.
Pierre
On Thu, Nov 25, 2010 at 3:35 PM, Yan Jiao wrote:
> Now it works after I update my R.
> Another question is can I pass the sample names as a parameter to sub select
> the samples for segmentation? instead of removing the unwanted ones from data
> folder?
>
> Many thanks
>
> yan
>
> -Original Message-
> From: aroma-affymetrix@googlegroups.com
> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
> Sent: 24 November 2010 17:06
> To: aroma-affymetrix
> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
> Ok, after seing your sessionInfo();
>
> You need to update to R v2.12.0, especially since you're on Windows
> 64-bit. Lots of work have been done by R core people to support
> Windows 64-bit on R v2.12.0 and beyond. There is no shortcut to this.
>
> Update aroma.affymetrix to v1.8.0, cf. http://aroma-project.org/install
>
> Also, the Cairo package is not available for the 64-bit version of R
> on Windows. If you try install.packages("Cairo") on your Windows
> machine, CRAN should report that package is not available. Either
> you have installed it by other means or it incorrectly installed on R
> v2.11.0.
>
> /Henrik
>
>
> On Wed, Nov 24, 2010 at 8:58 AM, Yan Jiao wrote:
>> Hi Henrik,
>>
>> I did what you suggested:
>>
>>> traceback()
>>
>> 13: stop(gettextf("package '%s' is not installed for 'arch=%s'",
>>
>> pkgname, r_arch), call. = FALSE, domain = NA)
>>
>> 12: testRversion(pkgInfo, package, pkgpath)
>>
>> 11: library(package, lib.loc = lib.loc, character.only = TRUE,
>> logical.return = TRUE,
>>
>> warn.conflicts = warn.conflicts, keep.source = keep.source)
>>
>> 10: base::require(...)
>>
>> 9: require("Cairo")
>>
>> 8: findPngDevice.default(transparent = FALSE)
>>
>> 7: findPngDevice(transparent = FALSE)
>>
>> 6: plot.CopyNumberSegmentationModel(model, path = path, imageFormat = "png",
>>
>> plotband = plotband, arrays = arrays, ...)
>>
>> 5: plot(model, path = path, imageFormat = "png", plotband = plotband,
>>
>> arrays = arrays, ...)
>>
>> 4: writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes =
>> chromosomes,
>>
>> zooms = zooms, ..., verbose = less(verbose))
>>
>> 3: writeGraphs(this, arrays = arrays, chromosomes = chromosomes,
>>
>> zooms = zooms, ..., verbose = less(verbose))
>>
>> 2: process.ChromosomeExplorer(ce.all, verbose = TRUE)
>>
>> 1: process(ce.all, verbose = TRUE)
>>
>>> sessionInfo()
>>
>> R version 2.11.0 (2010-04-22)
>>
>> x86_64-pc-mingw32
>>
>> locale:
>>
>> [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United
>> Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
>> LC_NUMERIC=C
>>
>> [5] LC_TIME=English_United Kingdom.1252
>>
>> attached base packages:
>>
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>>
>> [1] RColorBrewer_1.0-2 DNAcopy_1.22.1 preprocessCore_1.10.0
>> sfit_0.1.9 aroma.affymetrix_1.7.0 aroma.apd_0.1.7
>> affxparser_1.20.0
>>
>> [8] R.huge_0.2.0 aroma.core_1.7.0 aroma.light_1.16.1
>> matrixStats_0.2.2 R.rsp_0.4.0 R.cache_0.3.0
>> R.filesets_0.9.0
>>
>> [15] digest_0.4.2 R.utils_1.5.3 R.oo_1.7.4
>> R.methodsS3_1.2.1
>>
>> loaded via a namespace (and not attached):
>>
>> [1] tools_2.11.0
>>
>>>
>>
>> process(ce,chromosomes=c(1,8,17), verbose=-10)
>>
>> Generating ChromosomeExplorer report...
>>
>> Setting up ChromosomeExplorer report files...
>>
>> Copying template files...
>>
>> Source path:
>> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/includes
>>
>> Destination path: reports/includes
>>
>> Copying template files...done
>>
>> Setting up ChromosomeExplorer report files...done
>>
>> Explorer output version: 3
>>
>> Compiling ChromosomeExplorer.onLoad.js.rsp...
>>
>> Source:
>> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp
>>
>> Output path: reports/Fockens_1/ACC,-XY,RMA,+300,A+B,FLN,-XY
>>
>>
Re: [aroma.affymetrix] Problem with read CDF files
Hi Wero,
Dario is right, as explained in http://aroma-project.org/node/66.
Also, I would recommend not to manually add data in the installation
directories of R packages. When you upgrade to a new version of R,
your data will still be stuck in the installation directory of the old
version.
Specificially, I would avoid (1) having your 'annotationData' (and all
the others aroma.* folders) in the directory where aroma.affymetrix
is installed, and (2) using this installation directory as you working
directory.
See http://aroma-project.org/node/79 for an example of setup. Also,
remember that 'annotationData' in the working directory can be a
symbolic link to another directory on your file system.
Hope this helps,
Pierre
On Mon, Sep 27, 2010 at 5:05 PM, Dario Strbenac
wrote:
> Hello,
>
> You need to be in the directory above annotationData.
>
> - Dario.
>
> Original message
>>Date: Mon, 27 Sep 2010 16:53:06 -0700 (PDT)
>>From: aroma-affymetrix@googlegroups.com (on behalf of Wero
>>)
>>Subject: [aroma.affymetrix] Problem with read CDF files
>>To: "aroma.affymetrix"
>>Cc: ii...@inmegen.gob.mx
>>
>>Hi, I have been trying to read the CDF files for the HuGene-1_0-st-v1
>>array with aroma.affymetrix and it has been very confuse for me.
>>
>>I have the correct CDF files from the aroma page.
>>
>>The CDF files are in the path: "/Library/Frameworks/R.framework/
>>Versions/2.11/Resources/library/aroma.affymetrix/annotationData/
>>chipTypes/HuGene-1_0-st-v1".
>>
>>My working directory is: annotationData
>>
>>but I still have this error:
>>#
>>> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3")
>>Error in list(`AffymetrixCdfFile$byChipType(chipType, tags = "r3")` =
>>, :
>>
>>[2010-09-27 06:14:53] Exception: Could not locate a file for this chip
>>type: HuGene-1_0-st-v1,r3
>> at throw(Exception(...))
>> at throw.default("Could not locate a file for this chip type: ", pa
>> at throw("Could not locate a file for this chip type: ", paste(c(ch
>> at method(static, ...)
>> at AffymetrixCdfFile$byChipType(chipType, tags = "r3")
>>##
>>
>>Also, if I look for the cdf path file in R, it returns NULL
>>
>>>pathname <-
>>>"annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.cdf"
>>
>>> cdf <- AffymetrixCdfFile(pathname)
>>Error in list(`AffymetrixCdfFile(pathname)` = ,
>>`extend(AromaChipTypeAnnotationFile(...), c("AffymetrixCdfFile", ` =
>>, :
>>
>>[2010-09-27 06:48:54] Exception: Pathname not found: annotationData/
>>chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.cdf (none of the parent
>>directories [annotationData/chipTypes/HuGene-1_0-st-v1/] exist;
>>current directory is '/Library/Frameworks/R.framework/Versions/2.11/
>>Resources/library/aroma.affymetrix/annotationData/chipTypes/HuGene-1_0-
>>st-v1')
>> at throw(Exception(...))
>> at throw.default("Pathname not found: ", pathname, reason)
>> at throw("Pathname not found: ", pathname, reason)
>> at method(static, ...)
>> at Arguments$getReadablePathname(filename, path = path, mustExist =
>> at GenericDataFile(...)
>> at extend(GenericDataFile(...), "AromaMicroarrayDataFile")
>> at AromaMicroarrayDataFile(...)
>> at extend(AromaMicroarrayDataFile(...), c("AffymetrixFile", uses("A
>> at AffymetrixFile(...)
>> at extend(AffymetrixFile(...), "AromaChipTypeAnnotationFile")
>> at AromaChipTypeAnnotationFile(...)
>> at extend(AromaChipTypeAnnotationFile(...), c("AffymetrixCdfFile",
>> at Affymetrix
>>In addition: Warning messages:
>>1: In is.na(parent) :
>> is.na() applied to non-(list or vector) of type 'NULL'
>>2: In is.na(parent) :
>> is.na() applied to non-(list or vector) of type 'NULL'
>>> pathname <- getPathname(cdf)
>>> print(pathname)
>>[1] "annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-
>>v1,r3.cdf"
>>
>>> pathname2 <- AffymetrixCdfFile$findByChipType("HuGene-1_0-st-v1", tags="3")
>>> print(pathname2)
>>NULL
>>
>>###
>>This is my sessionInfo()
>>R version 2.11.1 (2010-05-31)
>>i386-apple-darwin9.8.0
>>
>>locale:
>>[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>
>>attached base packages:
>>[1] stats graphics grDevices utils datasets methods
>>[7] base
>>
>>other attached packages:
>> [1] oligoClasses_1.10.0 Biobase_2.8.0
>> [3] aroma.affymetrix_1.7.0 aroma.apd_0.1.7
>> [5] affxparser_1.20.0 R.huge_0.2.0
>> [7] aroma.core_1.7.0 aroma.light_1.16.1
>> [9] matrixStats_0.2.1 R.rsp_0.4.0
>>[11] R.cache_0.3.0 R.filesets_0.9.0
>>[13] digest_0.4.2 R.utils_1.5.2
>>[15] R.oo_1.7.4 oligo_1.12.2
>>[17] R.methodsS3_1.2.1
>>
>>loaded via a namespace (and not attached):
>>[1] affyio_1.16.0 Biostrings_2.16.5 DBI_0.2-5
>>[4] IRanges_1.6.6 preprocessCore_1.10.0 splines_2.11.1
>>[7] tools_2.11.1
>>
>>
>>This is my traceback()
>>6: throw.Exception(Exception(...))
>>5: throw(Exception(...))
>>4: throw.default(msg)
>>3: throw(msg)
Re: [aroma.affymetrix] GLAD not producing output
Hi Gene,
On Tue, Sep 7, 2010 at 4:38 PM, Gene wrote:
> I couldn't get any of the output methods to work to save my GLAD
> segmentation results (see output below). When I took a look at the
> auto-generated GLAD directory gladData/gsk,ACC,-XY,BPN,-XY,RMA,A
> +B,FLN,-XY/Mapping250K_Sty+Nsp, I saw that it was empty. I had been
> following along with the vignettes, so it's unclear to me what went
> wrong. If anyone can point out the problem, I would be very
> appreciative!
>
> Thanks.
>
>
>> glad <- GladModel(cesNs)
>
>> print(glad)
> GladModel:
> Name: cgh
> Tags: ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY
> Chip type (virtual): Mapping250K_Sty+Nsp
> Path: gladData/cgh,ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY/Mapping250K_Sty+Nsp
> Number of chip types: 2
> Sample & reference file pairs:
> Chip type #1 of 2 ('Mapping250K_Sty'):
> Sample data set:
> CnChipEffectSet:
> Name: cgh
> Tags: ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY
> Path: plmData/cgh,ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY/Mapping250K_Sty
> Platform: Affymetrix
> Chip type: Mapping250K_Sty,monocell
> Number of arrays: 205
> Names: X0283_Sty250, X0288_Sty250, ..., X8390_Sty250
> Time period: 2010-08-23 14:55:28 -- 2010-08-23 14:56:57
> Total file size: 2940.06MB
> RAM: 0.58MB
> Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
> combineAlleles: logi TRUE)
> Reference data set/file:
>
> Chip type #2 of 2 ('Mapping250K_Nsp'):
> Sample data set:
> CnChipEffectSet:
> Name: cgh
> Tags: ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY
> Path: plmData/cgh,ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY/Mapping250K_Nsp
> Platform: Affymetrix
> Chip type: Mapping250K_Nsp,monocell
> Number of arrays: 205
> Names: X0283_Nsp250, X0288_Nsp250, ..., X8390_Nsp250
> Time period: 2010-08-25 02:24:26 -- 2010-08-25 02:25:37
> Total file size: 3230.09MB
> RAM: 0.58MB
> Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
> combineAlleles: logi TRUE)
> Reference data set/file:
>
> RAM: 0.00MB
>
>> str(glad)
> Classes 'GladModel', 'CopyNumberSegmentationModel',
> 'CopyNumberChromosomalModel', 'ChromosomalModel', 'Object' atomic
> [1:1] NA
> ..- attr(*, ".env")=
> ..- attr(*, "...instantiationTime")= POSIXct[1:1], format:
> "2010-09-07 16:18:09"
>
>> rawCNs <- extractRawCopyNumbers(glad, array=1, chromosome=1)
>
> Error in list(`extractRawCopyNumbers(glad, array = 1, chromosome = 1)`
> = , :
>
> [2010-09-07 16:37:33] Exception: Argument 'x' is of length 1 although
> the range ([0,0]) implies that is should be empty.
> at throw(Exception(...))
> at throw.default(sprintf("Argument 'x' is of length %d although the
> range ([%s
> at throw(sprintf("Argument 'x' is of length %d although the range
> ([%s,%s]) im
> at getIndices.Arguments(static, ..., length = length)
> at getIndices(static, ..., length = length)
> at method(static, ...)
> at Arguments$getIndex(array, max = nbrOfArrays(this))
> at extractRawCopyNumbers.CopyNumberChromosomalModel(glad, array = 1,
> chromosom
> at extractRawCopyNumbers(glad, array = 1, chromosome = 1)
>
>
Did you fit the glad model before calling extractRawCopyNumbers, i.e.
fit(glad, verbose=verbose);
?
Pierre
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices datasets utils methods
> base
>
> other attached packages:
> [1] RColorBrewer_1.0-2 GLAD_2.10.0
> aroma.affymetrix_1.7.0
> [4] aroma.apd_0.1.7 affxparser_1.20.0
> R.huge_0.2.0
> [7] aroma.core_1.7.0 aroma.light_1.16.0
> matrixStats_0.2.1
> [10] R.rsp_0.3.6 R.cache_0.3.0
> R.filesets_0.8.3
> [13] digest_0.4.2 R.utils_1.4.4
> R.oo_1.7.3
> [16] R.methodsS3_1.2.0
>
> loaded via a namespace (and not attached):
> [1] tools_2.11.1
>
> --
> 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/
>
--
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/
Re: [aroma.affymetrix] Problems updating aroma.affymetrix
[Forwarding this to the list so that others can read this thread]
Pierre
On Wed, Sep 1, 2010 at 12:57 PM, Matt wrote:
> Hi Pierre,
>
> Thanks for the reply. I guess it's a problem with the source because what
> you say is exactly what I did and I get the error message shown.
>
> Best,
> Matt
>
> On Wed, Sep 1, 2010 at 3:20 PM, Pierre Neuvial
> wrote:
>>
>> Hi Matt,
>>
>> You want to *update* the package, not *patch* it: the difference
>> between updates and patches is explained at
>> http://aroma-project.org/howtos/updateOrPatch.
>>
>> So, to update aroma.affymetrix, do:
>>
>> source("http://aroma-project.org/hbLite.R";);
>> hbInstall("aroma.affymetrix");
>>
>> as explained at http://aroma-project.org/install
>>
>> Hope this helps,
>>
>> Pierre.
>>
>> On Wed, Sep 1, 2010 at 10:08 AM, Matt wrote:
>> > Hi there,
>> >
>> > I'd like to update my version of aroma.affymetrix, current version in
>> > use 0.9.1, so that I can utilize the new CN processing method. I
>> > followed the instructions on the site but I get the following error
>> > message
>> >
>> > Patching /home/matthew/.Rpatches/aroma.affymetrix/20080508/
>> > WeightsFile.R
>> > Failed to source:
>> > http://www.braju.com/R//patches/aroma.affymetrix/download.R
>> > Error in stop(ex$message) :
>> > Your version (0.9.1) of aroma.affymetrix is out of date. Please
>> > update.
>> > In addition: There were 11 warnings (use warnings() to see them)
>> >> sessionInfo()
>> > R version 2.7.0 Under development (unstable) (2008-01-21 r44087)
>> > x86_64-unknown-linux-gnu
>> >
>> > locale:
>> >
>> > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>> >
>> > attached base packages:
>> > [1] tools stats graphics grDevices datasets utils
>> > methods
>> > [8] base
>> >
>> > other attached packages:
>> > [1] Biobase_2.0.1 aroma.affymetrix_0.9.1
>> > aroma.apd_0.1.7
>> > [4] R.huge_0.2.0 digest_0.4.2
>> > aroma.light_1.16.1
>> > [7] affxparser_1.12.2 R.rsp_0.3.6
>> > R.cache_0.3.0
>> > [10] R.utils_1.5.0 R.oo_1.7.3 R.methodsS3_1.2.0
>> >
>> >
>> > How can I fix this?
>> >
>> > Thanks for any help.
>> > Mattt
>> >
>> > --
>> > 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/
>> >
>>
>> --
>> 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/
>
>
--
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/
Re: [aroma.affymetrix] Problems updating aroma.affymetrix
Hi Matt,
You want to *update* the package, not *patch* it: the difference
between updates and patches is explained at
http://aroma-project.org/howtos/updateOrPatch.
So, to update aroma.affymetrix, do:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
as explained at http://aroma-project.org/install
Hope this helps,
Pierre.
On Wed, Sep 1, 2010 at 10:08 AM, Matt wrote:
> Hi there,
>
> I'd like to update my version of aroma.affymetrix, current version in
> use 0.9.1, so that I can utilize the new CN processing method. I
> followed the instructions on the site but I get the following error
> message
>
> Patching /home/matthew/.Rpatches/aroma.affymetrix/20080508/
> WeightsFile.R
> Failed to source: http://www.braju.com/R//patches/aroma.affymetrix/download.R
> Error in stop(ex$message) :
> Your version (0.9.1) of aroma.affymetrix is out of date. Please
> update.
> In addition: There were 11 warnings (use warnings() to see them)
>> sessionInfo()
> R version 2.7.0 Under development (unstable) (2008-01-21 r44087)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tools stats graphics grDevices datasets utils
> methods
> [8] base
>
> other attached packages:
> [1] Biobase_2.0.1 aroma.affymetrix_0.9.1
> aroma.apd_0.1.7
> [4] R.huge_0.2.0 digest_0.4.2
> aroma.light_1.16.1
> [7] affxparser_1.12.2 R.rsp_0.3.6
> R.cache_0.3.0
> [10] R.utils_1.5.0 R.oo_1.7.3 R.methodsS3_1.2.0
>
>
> How can I fix this?
>
> Thanks for any help.
> Mattt
>
> --
> 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] Another "Exception: Cannot fit target function to enzyme"
Hi Gene Tastic,
On Mon, Aug 16, 2010 at 2:57 PM, Gene wrote:
> I'm getting the dreaded "Exception: Cannot fit target function to
> enzyme, because there are no (finite) data points that are unique to
> this enzyme" error, that has popped up a number of times on this board
> previously. However the usual problem, that fit(plm) wasn't run isn't
> the case here, so I'm stuck.
Thanks for checking this.
Can you update aroma.affymetrix to the most recent version (1.7.0):
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
and then paste the output of
verbose <- Arguments$getVerbose(-8)
ds <- lapply(chipTypes, function(x) {
doCRMAv2("gsk", chipType=x, plm="RmaCnPlm", verbose=verbose)
})
?
Thanks,
Pierre
> I've tried to run this the more
> automated way:
>
>
> chipTypes <- c("Mapping250K_Sty", "Mapping250K_Nsp")
> name <- 'gsk'
> ds <- lapply(chipTypes, function(x)
> doCRMAv2("gsk",chipType=x,verbose=-1, plm="RmaCnPlm"))
>
> or the more manual way:
>
> css <- lapply(chipTypes, function(x) AffymetrixCelSet$byName(name,
> chipType=x, verbose=T))
> css <- lapply(css, function(x) extract(x, !isDuplicated(x)))
> print(css)
> accs <- lapply(css, AllelicCrosstalkCalibration, model="CRMAv2")
> csCs <- lapply(accs, process, verbose=verbose)
> print(csCs)
> plms <- lapply(csCs, RmaCnPlm, mergeStrands=TRUE, combineAlleles=TRUE)
> print(plms)
> lapply(plms, fit, verbose=T)
> cess <- lapply(plms, getChipEffectSet)
> flns <- lapply(cess, FragmentLengthNormalization)
> cesns <- lapply(flns, process, verobse=-1)
>
> but either way I end up with something like this:
>
>
> Error in list(`lapply(flns, process, verobse = -1)` = ,
> `lapply.default(flns, process, verobse = -1)` = , :
>
> [2010-08-16 14:21:06] Exception: Cannot fit target function to enzyme,
> because there are no (finite) data points that are unique to this
> enzyme: 1
> at throw(Exception(...))
> at throw.default("Cannot fit target function to enzyme, because
> there are no (
> at throw("Cannot fit target function to enzyme, because there are no
> (finite)
> at getTargetFunctions.FragmentLengthNormalization(this, verbose =
> less(verbose
> at getTargetFunctions(this, verbose = less(verbose))
> at process.FragmentLengthNormalization(X[[1]], ...)
> at FUN(X[[1]], ...)
> at lapply.default(flns, process, verobse = -1)
> at lapply(flns, process, verobse = -1)
>
>
> Here is the output of sessionInfo():
>
>
> R version 2.11.1 (2010-05-31)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats graphics grDevices datasets utils methods
> base
>
> other attached packages:
> [1] preprocessCore_1.10.0 aroma.affymetrix_1.6.0
> aroma.apd_0.1.7
> [4] affxparser_1.20.0 R.huge_0.2.0
> aroma.core_1.6.0
> [7] matrixStats_0.2.1 R.rsp_0.3.6
> R.cache_0.3.0
> [10] R.filesets_0.8.2 digest_0.4.2
> aroma.light_1.16.0
> [13] R.utils_1.4.3 R.oo_1.7.3
> R.methodsS3_1.2.0
>
> loaded via a namespace (and not attached):
> [1] tools_2.11.1
> Warning message:
> 'DESCRIPTION' file has 'Encoding' field and re-encoding is not
> possible
>
>
> Any advice would be greatly appreciated!
>
>
> Thanks
> Gene
>
> --
> 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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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] Cannot fit normalization function to enzyme, because there are no (finite) data points that are unique to this enzyme: 1
Hi gouxiongpapa/felixli77quick,
See below.
On Thu, Aug 5, 2010 at 9:33 AM, gouxiongpapa wrote:
> Hi there
>
> I wonder some one could kindly help me out from this:
>
> I am trying to process a data set of affy snp 250K sty, and I just
> copied the steps in the vignette file: Estimation of total copy
> numbers using the CRMA v2 method (10K-GWS6), as below
>
>
> library(aroma.affymetrix)
> cdf <- AffymetrixCdfFile$byChipType("Mapping250K_Sty")
> gi <- getGenomeInformation(cdf)
> si <- getSnpInformation(cdf)
> acs <- AromaCellSequenceFile$byChipType(getChipType(cdf,
> fullname=FALSE))
> csv <- AffymetrixNetAffxCsvFile$byChipType("Mapping250K_Sty", tag ="")
> csR <- AffymetrixCelSet$fromFiles(path2[1], cdf=cdf)
> acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
> csC <- process(acc, verbose=verbose)
> bpn <- BasePositionNormalization(csC, target="zero")
> csN <- process(bpn, verbose=verbose)
> plm <- AvgCnPlm(csN, mergeStrands=TRUE, combineAlleles=TRUE)
Here you forgot
fit(plm, verbose=TRUE)
FYI this has been discussed several times on the list, see e.g.
http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/6dfe3afc216f27fc/34442574ee1b039a
Pierre
> ces <- getChipEffectSet(plm)
> fln <- FragmentLengthNormalization(ces, target="zero")
> cesN <- process(fln, verbose=verbose)
>
>
> !!
> I got straight down here and got an error
> Error in list(`process(fln, verbose = -1)` = ,
> `process.FragmentLengthNormalization(fln, verbose = -1)` =
> , :
>
> [2010-08-05 12:22:33] Exception: Cannot fit normalization function to
> enzyme, because there are no (finite) data points that are unique to
> this enzyme: 1
>
> I attached the entire screen below
> !
> ceR <- getAverageFile(cesN, verbose=verbose)
>
>
>
>
> Normalizing set for PCR fragment-length effects...
> Identifying SNP and CN units...
> types
> 2
> 238378
> subsetToUpdate:
> int [1:238378] 1 2 3 4 5 6 7 8 9 10 ...
> Identifying SNP and CN units...done
> Retrieving SNP information annotations...
> DChipSnpInformation:
> Name: Mapping250K_Sty snp info
> Tags:
> Full name: Mapping250K_Sty snp info
> Pathname: annotationData/chipTypes/Mapping250K_Sty/Mapping250K_Sty
> snp info.txt
> File size: 24.00 MB (25164292 bytes)
> RAM: 17.28 MB
> Chip type: Mapping250K_Sty
> Number of enzymes: 1
> Retrieving SNP information annotations...done
> Identifying the subset used to fit normalization function(s)...
> int [1:233552] 1 2 3 4 5 6 7 8 9 10 ...
> Identifying the subset used to fit normalization function(s)...done
> Shift: 0
> onMissing: median
> Array #1 of 49
> ('CLONE_p_STY29_(CO-106422)_Mapping250K_Sty_A09_104500')...
> V1
> Min. : 115
> 1st Qu.: 440
> Median : 598
> Mean : 609
> 3rd Qu.: 771
> Max. :1093
> NA's : 78
> int [1:233552] 1 2 3 4 5 6 7 8 9 10 ...
> Getting cell matrix map...
> 'UnitGroupCellMatrixMap' int [1:238378, 1] 1 2 3 4 5 6 7 8 9
> 10 ...
> Getting cell matrix map...done
> Getting theta estimates...
> num [1:238378, 1] 0 0 0 0 0 0 0 0 0 0 ...
> V1
> Min. :0
> 1st Qu.:0
> Median :0
> Mean :0
> 3rd Qu.:0
> Max. :0
> Getting theta estimates...done
> Calculating total signals...
> Total thetas:
> num [1:238378] 0 0 0 0 0 0 0 0 0 0 ...
> Calculating total signals...done
> Normalizing log2 signals...
> Log2 signals:
> num [1:238378] -Inf -Inf -Inf -Inf -Inf ...
> Error in list(`process(fln, verbose = -1)` = ,
> `process.FragmentLengthNormalization(fln, verbose = -1)` =
> , :
>
> [2010-08-05 12:22:33] Exception: Cannot fit normalization function to
> enzyme, because there are no (finite) data points that are unique to
> this enzyme: 1
> at throw(Exception(...))
> at throw.default("Cannot fit normalization function to enzyme,
> because there a
> at throw("Cannot fit normalization function to enzyme, because there
> are no (f
> at normalizeFragmentLength.default(y, fragmentLengths = fl,
> targetFcns = targe
> at normalizeFragmentLength(y, fragmentLengths = fl, targetFcns =
> targetFcns, s
> at process.FragmentLengthNormalization(fln, verbose = -1)
> at process(fln, verbose = -1)
> Normalizing log2 signals...done
> Array #1 of 49
> ('CLONE_p_STY29_(CO-106422)_Mapping250K_Sty_A09_104500')...done
> Normalizing set for PCR fragment-length effects...done
>
> --
> 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] Analysis of GenomeWideSNP6.0 data
Hi, On Tue, Aug 3, 2010 at 8:12 AM, Ajanthah Sangaralingam wrote: > Thank you for the reply. I actually need to get the log2 copy number ratios > form the raw .cel files of a GenomeWideSNP6.0 array - I was using CRMA1 but > am now repeating the analysis using CRMA v2. > I am putting all of the different tumour types either matched or unmatched > with a germline sample in the same directory and all the normal samples in > another directory. This is fine, but note that did not need to put them in separate directories. > I will then go through the processes of qulaity assesment, calibration > crosstalk, normalization for probe sequence effect, probe summarization, and > normalization of PCR fragment length effects. > > Do I need to calculate the raw copy numbers and turn these into log2 copy > numbers? I don't understand your question. > How would I then calculate the copy numbers for > 1. Unpaired tumour samples - will need to be compared to a pooled reference > from a particular tumpur type > 2. Paired samples? It's hard to be more specific than what Henrik already said without more details on your sample names and tumor types, and most importantly on the design of your study. I'll try for the unpaired analysis (your 1.) I am assuming that you have two data sets: - 'dsT' for the tumor samples, - 'dsN' for the normal samples. It seems that your concern is to use *tumor-type specific* sets of normal samples. Is that correct ? See my remark below on the fact that I'm not sure it's what you should do. If so, then assuming that 'idxT1' contains the indices of all tumor samples from a particular tumor type in dsT, and 'idxN1' contains the indices of normal samples from the same tumor type in dsN, you can do dsN1 <- extract(dsN, idxN1); ## normal samples of tumor type 1 dsT1 <- extract(dsT, idxT1); ## tumor samples of tumor type 1 dfR1 <- getAverageFile(dsN1);## pool of normal samples of tumor type 1 sm1 <- CbsModel(dsT1, dfR1); Then you can do fit(sm1, chromosome=1, array=1, verbose=log); to perform CBS segmentation and/or rawCNs1 <- extractRawCopyNumbers(sm1, array=1, chromosome=1) plot(rawCns1) to extract and plot raw copy numbers (independently of CBS). And so on for each tumor type. This should answer your 1. However, I'm not sure that using tumor-type specific sets of normal samples will give you better results. This depends in particular on the following specific points in your design: - Are you "normals" normal tissue samples blood samples ? - Were all the tumor and normal microarrays done in the same lab, and approximately at the same time ? If so, combining all the normals could be better. One way to know which option is best (tumor-specific reference or global reference) is to try both and compare the segmentation results (e.g. using ChromosomeExplorer). For your 2 (paired tumor/normal analysis), I think Henrik gave all the necessary information already, but assuming that 'idxT2' contains the indices of all tumor samples from a particular tumor type in dsT that have a paired normal, and 'idxN2' contains the indices of these paired normal samples from the same tumor type in dsN, further assuming that *the samples are in the same order in the two sets of indices*, you can do dsN2 <- extract(dsN, idxN2); dsT2 <- extract(dsT, idxT2); sm2 <- CbsModel(dsT2, dsN2); fit(sm2, chromosome=1, array=1, verbose=log); rawCNs2 <- extractRawCopyNumbers(sm2, array=1, chromosome=1) plot(rawCNs2); I hope this helps, Pierre. > > Many thanks for your help > > On 18/07/2010 12:01, "Ajanthah Sangaralingam" > wrote: > >> Hi, >> >> Yes this is correct. >> >> Many thanks >> >> Ajanthah >> >> From: aroma-affymetrix@googlegroups.com [aroma-affymet...@googlegroups.com] >> On >> Behalf Of Henrik Bengtsson [...@stat.berkeley.edu] >> Sent: Sunday, July 18, 2010 11:28 AM >> To: aroma-affymetrix >> Subject: Re: [aroma.affymetrix] Analysis of GenomeWideSNP6.0 data >> >> Hi. >> >> On Fri, Jul 16, 2010 at 11:13 AM, Ajanthah Sangaralingam >> wrote: >>> Hi, >>> >>> I have been doing some paired total copy number analysis in aroma >>> afyymetrix. >>> The dataset I have is complicated for haf the dataset I have reference >>> samples, for the other half I will do an unpiared analysis. >> >> So, to make sure I don't misunderstand, you have an Affymetrix >> GenomeWideSNP_6 (GWS6) data set that contains tumors and for some, but >> not all of the you have matched normal samples, where "matched normal" >> mean a normal tissue or normal blood extract from the same patient as >> the tumor was taken. Is this correct? >> >>> I alos have data from many different tomor types not just one - I do not >>> have >>> the sample number of samples from each type of tumor. >>> >>> My questions are: >>> >>> When doing a paired analysis - the normal and tumour data have there own >>> directories and allelic cross talk calibration, summarization and PCR >>> fragment le
Re: [aroma.affymetrix] Error need help(CdfFile$byChipType)
Hi,
Most probably you haven't put the required CDF file in the
corresponding annotationData/chipTypes/ directory.
Have you read the vignette http://aroma-project.org/node/38 ? This is
well explained there.
Also, similar versions of this question have been answered on this
list, see for example
http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/d992f2ca51e71774/8ba42bb7bdbf1b48
Best
Pierre.
Be sure to put the CDF file in your annotationData/chipTypes/XX/ where
XX is the platform you are using (e.g. HuGene-1_0-st-v1 for Human
Gene 1.0 ST, HT_HG-U133_Plus_PM for the human PM plate arrays, etc.)
On Tue, Aug 3, 2010 at 2:27 PM, vish wrote:
>
> I am really new to this aroma.affymetrix. I am trying to analyze
> HuGene-1_0-st-v1 array and interested in Quality control check/
> Assessment.
> when I am trying to run this command I am ending up with this error .
> Any help is greatly appreciated.
>
> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3")
> Error in list(`AffymetrixCdfFile$byChipType(chipType, tags = "r3")` =
> , :
>
> [2010-08-03 16:23:44] Exception: Could not locate a file for this chip
> type: HuGene-1_0-st-v1,r3
> at throw(Exception(...))
> at throw.default("Could not locate a file for this chip type: ",
> paste(c(chipType, tags), collapse = ","))
> at throw("Could not locate a file for this chip type: ",
> paste(c(chipType, tags), collapse = ","))
> at method(static, ...)
> at AffymetrixCdfFile$byChipType(chipType, tags = "r3")
>
> Ashwin
>
> --
> 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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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] attach two data frames
Hi Viking, Note that your question has nothing to do with aroma.* packages, so it should not be posted on this list. In this particular case, I think the function to use is Google search :) http://www.google.com/search?q=combine+data+frame Pierre On Thu, Jul 15, 2010 at 10:52 AM, Liang Cheng wrote: > Hello, > I have two data frames, and I want to combine them together, that means I > want to put one after the bottom of the other. > For example, I have a data frame x, y > > x: > > column name: A B C > 1 1 3 > 3 5 6 > y: > > column name:A F G > 3 9 1 > 8 7 0 > > I want to get a new data frame like this: > > A B C > 1 1 3 > 3 5 6 > 3 9 1 > 87 0 > > what function should I use? > thanks a lot：） > > Viking > > -- > 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/ > -- 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/
Re: [aroma.affymetrix] uncomplete extractDataFrame()
Hi,
One comment below.
On Wed, Jul 7, 2010 at 11:15 PM, Pierre Neuvial
wrote:
> Hi Emilie,
>
> Sorry for taking such a long time to reply.
>
> You are right: there was a bug in
> AromaUnitSignalBinarySet.writeDataFrame causing the same data chunk to
> be written several times. This bug will be fixed in the next realease
> of aroma.core. In the meantime, Henrik has provided a patch: to
> download and install it, just do
>
> library("aroma.affymetrix");
> downloadPackagePatch("aroma.core");
>
> as (now) explained in http://aroma-project.org/howtos/updateOrPatch.
>
> Then
>
> dfTxt <- writeDataFrame(ds$fracB, columns=c("unitName", "chromosome",
> "position", "*"))
I just wanted to add that in general it's better to use the verbose
output, as in:
log <- Arguments$getVerbose(-8, timestamp=TRUE)
dfTxt <- writeDataFrame(ds$fracB, columns=c("unitName", "chromosome",
"position", "*"), verbose=log)
(that's how I located the bug)
Pierre
>
> should give you the txt file you expect. Let us know if it works for you.
>
> Ouf !
>
> Pierre
>
> On Fri, Jul 2, 2010 at 6:35 AM, Emilie T wrote:
>>
>> Bonjour Pierre,
>> Thank you for your response and and sorry for the mistake in the title of
>> the subject.
>> Of course my question is about the writeDataFrame() function.
>> Thank you for the help on "ds" object creation. This point seems to be ok
>> now but I have re-deleted the txt objects and re-try to build the txt object
>> and I still have the same problem. This is very strange.
>> I can see in your exemple that you also obtain duplicated rows in your
>> matrix. your "d" object contain 200 rows and your "unique(d)"
>> only 50. Your matrix is duplicated 4 times in your case.
>> Why this row duplication ?
>> I see that you alo seems to use the Affy SNP 6 chip in your example. I
>> suppose that we don't have the same number of raws because you certainly
>> don't use the same annotation file.
>> The Affy 6 SNP have about 200 unique unitNames (about 1M SNP + 1M CNV).
>> So in your case as in mine I expect to have as unique(d) object a matrix
>> with about 2M unique unitNames (or 1M if you consider that CNV units are non
>> relevant for fracB calculation).
>> When I compare the 'd' object unitNames to the Affy SNP 6 annotation matrix
>> (see my code bellow), I see that there is several missing unitNames. In
>> fact, only the first ones are presents in my "d" object.
>> Do you know how to obtain the fracB measurement for this missing unitNames?
>> Thank you very much for your help.
>> Here is the complete code :
>> > str(ds)
>> List of 2
>> $ total:Classes 'AromaUnitTotalCnBinarySet', 'CopyNumberDataSet',
>> 'AromaUnitSignalBinarySet', 'AromaTabularBinarySet',
>> 'GenericTabularFileSet', 'GenericDataFileSet', 'FullNameInterface', 'Object'
>> atomic [1:1] NA
>> .. ..- attr(*, ".env")=
>> .. ..- attr(*, "...instantiationTime")= POSIXct[1:1], format: "2010-07-02
>> 10:46:48"
>> $ fracB:Classes 'AromaUnitFracBCnBinarySet', 'AromaUnitSignalBinarySet',
>> 'AromaTabularBinarySet', 'GenericTabularFileSet', 'GenericDataFileSet',
>> 'FullNameInterface', 'Object' atomic [1:1] NA
>> .. ..- attr(*, ".env")=
>> .. ..- attr(*, "...instantiationTime")= POSIXct[1:1], format: "2010-07-02
>> 10:46:49"
>> > dfTxt <- writeDataFrame(ds$fracB, columns=c("unitName", "chromosome",
>> > "position", "*"))
>> > d <- readDataFrame(dfTxt)
>> > str(d)
>> 'data.frame': 1857154 obs. of 17 variables:
>> $ unitName : Factor w/ 71429 levels "AFFX-5Q-123",..: 1 2 3 4 487 490
>> 493 496 499 502 ...
>> $ chromosome : int NA NA NA NA NA NA NA NA NA NA ...
>> $ position : int NA NA NA NA NA NA NA NA NA NA ...
>> $ A,fracB : num NA NA NA NA NA NA NA NA NA NA ...
>> $ B,fracB : num NA NA NA NA NA NA NA NA NA NA ...
>> $ C,fracB : num NA NA NA NA NA NA NA NA NA NA ...
>> $ D,fracB : num NA NA NA NA NA NA NA NA NA NA ...
>> $ E,fracB : num NA NA NA NA NA NA NA NA NA NA ...
>> $ F,fracB : num NA NA NA NA NA NA NA NA NA NA ...
>> $ G,fracB : num NA NA NA NA NA NA NA NA NA NA ...
>> $ H,fracB :
Re: [aroma.affymetrix] uncomplete extractDataFrame()
$ : chr "unitName" "chromosome" "position" "A,fracB" ...
> .. ..$ : chr "AFFX-5Q-123" "NA" "NA" "NA" ...
> .. ..$ : chr "AFFX-5Q-456" "NA" "NA" "NA" ...
> .. ..$ : chr "AFFX-5Q-789" "NA" "NA" "NA" ...
> .. ..$ : chr "AFFX-5Q-ABC" "NA" "NA" "NA" ...
> .. ..$ : chr "AFR_A02_SB" "NA" "NA" "NA" ...
> .. ..$ : chr "AFR_A04_SB" "NA" "NA" "NA" ...
> .. ..$ : chr "AFR_A06_SB" "NA" "NA" "NA" ...
> .. ..$ : chr "AFR_A08_SB" "NA" "NA" "NA" ...
> .. ..$ : chr "AFR_A10_SB" "NA" "NA" "NA" ...
> ..$ columns : chr "unitName" "chromosome" "position" "A,fracB" ...
> > str(unique(d))
> 'data.frame': 71429 obs. of 17 variables:
> $ unitName : Factor w/ 71429 levels "AFFX-5Q-123",..: 1 2 3 4 487 490
> 493 496 499 502 ...
> $ chromosome : int NA NA NA NA NA NA NA NA NA NA ...
> $ position : int NA NA NA NA NA NA NA NA NA NA ...
> $ A,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ B,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ C,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ D,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ E,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ F,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ G,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ H,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ I,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ J,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ K,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ L,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ M,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ N,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> - attr(*, "fileHeader")=List of 6
> ..$ comments: chr "# name: data" "# tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY"
> "# fullName: data,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY" "# nbrOfFiles: 14" ...
> ..$ sep : chr "\t"
> ..$ quote : chr "\""
> ..$ skip : num 0
> ..$ topRows :List of 10
> .. ..$ : chr "unitName" "chromosome" "position" "A,fracB" ...
> .. ..$ : chr "AFFX-5Q-123" "NA" "NA" "NA" ...
> .. ..$ : chr "AFFX-5Q-456" "NA" "NA" "NA" ...
> .. ..$ : chr "AFFX-5Q-789" "NA" "NA" "NA" ...
> .. ..$ : chr "AFFX-5Q-ABC" "NA" "NA" "NA" ...
> .. ..$ : chr "AFR_A02_SB" "NA" "NA" "NA" ...
> .. ..$ : chr "AFR_A04_SB" "NA" "NA" "NA" ...
> .. ..$ : chr "AFR_A06_SB" "NA" "NA" "NA" ...
> .. ..$ : chr "AFR_A08_SB" "NA" "NA" "NA" ...
> .. ..$ : chr "AFR_A10_SB" "NA" "NA" "NA" ...
> ..$ columns : chr "unitName" "chromosome" "position" "A,fracB" ...
>
> > unique(table(d$unitName))
> [1] 26
> As I say in my first message, I have controled wich units are missing with
> the annotation matrix :
> > ugp <- AromaUgpFile$byChipType("GenomeWideSNP_6");
> > ugp
> AromaUgpFile:
> Name: GenomeWideSNP_6
> Tags: na30,hg18,HB20100215
> Full name: GenomeWideSNP_6,na30,hg18,HB20100215
> Pathname:
> annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,na30,hg18,HB20100215.ugp
> File size: 8.85 MB (9281130 bytes)
> RAM: 0.00 MB
> Number of data rows: 1856069
> File format: v1
> Dimensions: 1856069x2
> Column classes: integer, integer
> Number of bytes per column: 1, 4
> Footer: 20100215 21:16:37
> CETAffymetrixGenomeWideSNP_6Henrik
>
> Bengtssonh...@aroma-project.orgGenomeWideSNP_6.cdf484489553223f3cd9141404b2a926a40cf47d6f1aGenomeWideSNP_6,Full.cdf4932917453fbe0f6e7c8a346105238a3f3d10d4ecGenomeWideSNP_6,Full,na30,hg18,HB20100215.ugp9407867446e0ff43fbe9650ab48aa41ecee6bec
> Chip type: GenomeWideSNP_6
> Platform: Affymetrix
> > ugpTxt <- writeDataFrame(ugp, columnNamesPrefix="none");
> > ugpTxt
> TabularTextFile:
> Name: GenomeWideSNP_6
> Tags: na30,hg18,HB20100215.ugp
> Full name: GenomeWideSNP_6,na30,hg18,HB20100215.ugp
> Pathname:
> annotationData,txt/Geno
Re: [aroma.affymetrix] Aroma Affymetrix package update problem
Hi Fong,
On Tue, Jul 6, 2010 at 11:19 AM, Fong wrote:
> Hi,
>
> I've been trying to update my aroma affymetrix installation to the
> latest version and I was running the command,
>
> downloadPackagePatch("aroma.affymetrix")
>
> but I run into these errors.
>
> Failed to source: http://www.braju.com/R//patches/aroma.core/download.R
> Error in stop(ex$message) :
> Your version (1.4.0) of aroma.core is out of date. Please update.
> In addition: There were 36 warnings (use warnings() to see them)
>
> Any ideas on how to fix this?
The error message says you should *update* before *patching*, ie first do
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
Then you will have the latest version of the package, and you can patch it as:
library("aroma.affymetrix");
downloadPackagePatch("aroma.affymetrix")
For the record this is explained in
http://aroma-project.org/howtos/updateOrPatch
I hope this helps.
Pierre
>
> --
> 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/
>
--
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] uncomplete extractDataFrame()
Salut Emilie,
On Thu, Jul 1, 2010 at 10:13 AM, EmilieT wrote:
> Hello,
>
> I am using your R framework with a set of Affymetrix SNP 6 data and I
> have a problem with the extractDataFrame function.
> The result is an incomplete matrix with row duplication.
>
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] fr_FR.UTF-8/fr_FR.UTF-8/C/C/fr_FR.UTF-8/fr_FR.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods
> base
>
> other attached packages:
> [1] aroma.cn_0.5.0 aroma.affymetrix_1.6.0
> aroma.apd_0.1.7 affxparser_1.20.0 R.huge_0.2.0
> [6] aroma.core_1.6.0 matrixStats_0.2.1
> R.rsp_0.3.6 R.cache_0.3.0 R.filesets_0.8.2
> [11] digest_0.4.2 R.utils_1.4.0
> R.oo_1.7.2 aroma.light_1.16.0 R.methodsS3_1.2.0
>
> I use the standard doCRMAv2 function :
> > ds <- doCRMAv2("data",
> chipType="GenomeWideSNP_6",combineAlleles=FALSE);
>
>> ds
> $total
> AromaUnitTotalCnBinarySet:
> Name: data
> Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
> Full name: data,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
> Number of files: 14
> Names: A,B, ..., C [14]
> Path (to the first file): totalAndFracBData/data,ACC,ra,-XY,BPN,-
> XY,AVG,FLN,-XY/GenomeWideSNP_6
> Total file size: 99.13 MB
> RAM: 0.02MB
>
> $fracB
> AromaUnitFracBCnBinarySet:
> Name: data
> Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
> Full name: data,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
> Number of files: 14
> Names: A,B, ..., C [14]
> Path (to the first file): totalAndFracBData/data,ACC,ra,-XY,BPN,-
> XY,AVG,FLN,-XY/GenomeWideSNP_6
> Total file size: 99.13 MB
> RAM: 0.02MB
>
> It seems to be impossible to use this 'ds' object (or ds$fracB or ds
> $total) as an entrance for the extractDataFrame() function.
Yes: this is because extractDataFrame is meant to extract *chip
effects* (http://aroma-project.org/howtos/extractDataFrame) in your
case total and allele-specific *intensities*, and your ds$total and
ds$fracB are already one step further in the analysis: they are
AromaUnit*CnBinaryFile:s. For these you can use writeDataFrame
(http://aroma-project.org/howtos/writeDataFrame) as you seem to be
doing below.
> So I must do :
>
>> rootPath <- "totalAndFracBData"
>> dataSet <- "data,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY"
>> ds <- AromaUnitFracBCnBinarySet$byName(dataSet, chipType="GenomeWideSNP_6",
>> paths=rootPath);
>> ds
> AromaUnitFracBCnBinarySet:
> Name: data
> Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
> Full name: data,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
> Number of files: 14
> Names: A,B, ..., C [14]
> Path (to the first file): totalAndFracBData/data,ACC,ra,-XY,BPN,-
> XY,AVG,FLN,-XY/GenomeWideSNP_6
> Total file size: 99.13 MB
> RAM: 0.02MB
You don't really to do this: your new 'ds' is exactly your previous
'ds$fracB' (more on this below).
>
> When I use the extractDataFrame function, I obtain the folowing
> object :
Below you are using writeDataFrame, not extractDataFrame. Right ?
>
>> dfTxt <- writeDataFrame(ds, columns=c("unitName", "chromosome", "position",
>> "*"))
>> d <- readDataFrame(dfTxt)
>> str(d)
> 'data.frame': 1857154 obs. of 17 variables:
> $ unitName : Factor w/ 71429 levels
> "AFFX-5Q-123",..: 1 2 3 4 487 490 493 496 499 502 ...
> $ chromosome : int NA NA NA NA NA NA NA NA NA NA ...
> $ position : int NA NA NA NA NA NA NA NA NA
> NA ...
> $ A,fracB : num NA NA NA NA NA NA NA NA NA
> NA ...
> $ B,fracB : num NA NA NA NA NA NA NA NA NA
> NA ...
> $ C,fracB : num NA NA NA NA NA NA NA NA NA
> NA ...
> $ ...
>
> First of all, you can see that there is only the fracB columns. The
> first "ds" object had a "total" item, it seems to have been lost. The
> directory
> /totalAndFracBData/data,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY/GenomeWideSNP_6
> also contain the ,total.asb files. There is maybe a problem with
> my new 'ds' object (which refers to only 14 files).
Yes, this is expected because your new 'ds' has been created using
ds <- AromaUnitFracBCnBinarySet$byName(dataSet,
chipType="GenomeWideSNP_6", paths=rootPath);
As the "FracB" indicates, this 'ds' only contains allele B fractions. You can do
totalDs <- AromaUnitTotalCnBinarySet$byName(dataSet,
chipType="GenomeWideSNP_6", paths=rootPath);
to get the corresponding total CN data.
>
> There is also a problem of row duplication : you can see that the
> number of row is the same as Affymetrix SNP 6 number of units (so the
> result seems to be good).
Well, I've tried to reproduce what you have and I'm getting 200 rows:
> str(d);
'data.frame': 200 obs. of 5 variables:
$ unitName : Factor
w/ 50 levels "AFFX-5Q-123",..: 1 2 3 4 487 490 493 496 499 502 ...
$ chromosome : int
NA NA NA NA NA NA NA NA NA NA ...
$ position
Re: [aroma.affymetrix] Microsoft Visual C++ Runtime Library
Thanks, and when do you get an error ? Can you paste the error message
and the output of traceBack() ?
Pierre
On Thu, Jul 1, 2010 at 10:26 AM, Liang Cheng wrote:
> Thank you, Pierre,
> the following is the sessionInfo and code:
>
> R version 2.11.0 (2010-04-22)
> i386-pc-mingw32
> 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] preprocessCore_1.10.0 aroma.affymetrix_1.6.0 aroma.apd_0.1.7
> [4] affxparser_1.20.0 R.huge_0.2.0 aroma.core_1.6.0
> [7] aroma.light_1.16.0 matrixStats_0.2.1 R.rsp_0.3.6
> [10] R.cache_0.3.0 R.filesets_0.8.2 digest_0.4.2
> [13] R.utils_1.4.2 R.oo_1.7.3 R.methodsS3_1.2.0
>
> Code:
>
> library(aroma.affymetrix)
> cs <- AffymetrixCelSet$byName("1",
> chipType="Mapping250K_Nsp")
> qn <- QuantileNormalization(cs)
> csQN <- process(qn, verbose=TRUE)
> plm <- RmaCnPlm(csQN, combineAlleles=TRUE, mergeStrands=TRUE)
> fit(plm, verbose=TRUE)
> ces <- getChipEffectSet(plm)
> exData <- extractDataFrame(ces, units=NULL, addNames=TRUE)
> write.table(exData,file="fileName.txt",row.names=FALSE)
>
> thank you very much,
>
> Liang
>
>
> 2010/7/1 Pierre Neuvial
>>
>> Hi,
>>
>> Could you please report the output of sessionInfo() and traceback(),
>> and post a complete code example ?
>>
>> Pierre
>>
>> On Tue, Jun 29, 2010 at 10:09 AM, Liang Cheng
>> wrote:
>> > Hello everyone,
>> > I meet this error when I try to read 10 CEL files by using
>> > AffymetrixCelSet:
>> >
>> > the application has requested the runtime to terminate it in an unusaul
>> > way.
>> >
>> > Can someone help me？
>> > thanks a lot,
>> > Liang
>> >
>> > --
>> > 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/
>> >
>>
>> --
>> 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/
>
> --
> 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/
>
--
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/
Re: [aroma.affymetrix] Microsoft Visual C++ Runtime Library
Hi, Could you please report the output of sessionInfo() and traceback(), and post a complete code example ? Pierre On Tue, Jun 29, 2010 at 10:09 AM, Liang Cheng wrote: > Hello everyone, > I meet this error when I try to read 10 CEL files by using AffymetrixCelSet: > > the application has requested the runtime to terminate it in an unusaul way. > > Can someone help me？ > thanks a lot, > Liang > > -- > 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/ > -- 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/
Re: [aroma.affymetrix] question about aroma on Affy SNPchip 6.0
Hi Davide,
On Wed, May 12, 2010 at 5:32 AM, Davide Cora' wrote:
> Dear all,
>
> we are writing this email regarding the usage of the R package AROMA
> on an Affymetrix SNPChip 6.0 platform.
>
> We are currently using the Aroma Affy package to analyze a
> snpCHIP Affy 6.0 dataset, following the instructions in
> the corresponding Vignette from the website:
> http://www.aroma-project.org/node/15.
>
> Even if the instructions for the Affy 6.0 are labeled as
> "desprecated" we were able to perform a complete analysis
> forkflow with our dataset composed by 55 .CEL files.
Yes, it's working, it's just that there is a newer version of the
method available, see your 4) below.
>
> We have a couple of questions regarding this analysis, and we
> are grateful to get suggestions relative to that points.
>
> 1) following the Vignette, we completed the analysis using
> as referece, the one calculated directly from the data
> ("common reference is by default calculated as the robust
> average across samples"). Is it possible to set an external
> custom reference ? In particular, we are interested in the
> possibility to use as reference the one provided directly
> by Affymentrix, for example, in the GenoType Console.
>
This is possible, but not recommended, as you would introduce
lab/batch/experiment variability by using references from another lab.
Internal references (from the same lab, possibly even from the same
batch of experiments) generally give you a better signal to noise
ratio.
If you still want to use external references, that's possible. It is
easy if they are normalized within aroma.affymetrix (once you have a
CnChipEffectSet for them, you can do for example
glad <- GladModel(ces1, ces2)
where ces1 is your test CnChipEffectSet and ces2 your (new) refrence
CnChipEffectSet.
Using references which have not been normalized using aroma.affymetrix
is also possible, but not as easy because we have not yet written
wrappers to
to create objects of class 'CopyNumberChromosomalModel' from external
files yet. FYI this is one of our future plans, see
http://aroma-project.org/features/future
> 2) we are interested in performing the Glad analysis
> implemented in the Aroma package, but importing log2ratio data
> calculated from external software. Is it possible to do that ?
Same answer: yes, it is possible, but not easy currently, because
there are no wrappers to create objects of class 'GladModel' from
external files yet. Also see http://aroma-project.org/features/future
Currently the quickest way to go is probably to use the GLAD package directly.
>
> 3) we extracted raw data obtained within the analysis according to the
> Vignette by means of the "extractRawCopyNumbers" method.
> Which is the reference genome for this analys ?
The reference used by extractRawCopyNumbers is the reference defined
in the first argument (ie an object of class
CopyNumberChromosomalModel). going back to the example in the
vignette you have been looking at:
rawCNs <- extractRawCopyNumbers(cbs, array=1, chromosome=1)
Here the reference used is the one defined in the object 'cbs'. In
your case I guess it is the robust average across samples.
> Are the positional
> data compatible with the ones provided by the Affymetrix GenoType
> Console ?
Unit positions are retrieved from the UGP file that you have specified
in your analysis. The most recent UGP files for a given chip type are
on the corresponding page, in your case:
http://aroma-project.org/chipTypes/GenomeWideSNP_6
These files have been generated using Affymetrix' NetAffx CSV files,
and I think this is the information used by Genotype Console. Make
sure that they correspond to the same genome build.
>
> 4) as we told before, we performed successfully a
> complete analysis using the deprecated vignette for the
> affy 6.0 chip. Are there any updated version of the Aroma
> and corresponding Vignette for such type of data ?
> Do you
> think the Aroma package will be further maintained in the future for
> that type of platform ?
Yes, see the CRMAv2 method: http://www.aroma-project.org/vignettes/CRMAv2
Note: this vignette is explicitly referred to in the vignette you have
looked at. Did you see this reference ? Let us know if we can make
this clearer.
Hope this helps.
Pierre
>
> Thank you in advance for your attention :-)
>
> Davide
>
>
>
> --
> ---
>
> Davide Cora',
>
> email: davide.c...@ircc.it
> davide.c...@gmail.com
> web: http://www.to.infn.it/~cora/
> ---
>
> --
> 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-affymetr
Re: [aroma.affymetrix] re: chipEffects getAverage = 0?
Hi Seth, On Thu, Feb 18, 2010 at 5:32 AM, seth redmond wrote: > I seem to be having some trouble generating an average file for a chip > effects set. I'm following the CRMA2 vignette (skipping the fragment lengths > normalisation). The CES seems to be generated OK, but getAverage returns '0' > for all values. Any ideas why? missing the frag-length normalisation > shouldn't affect this should it? No, it shouldn't. Can you post your entire script and your sessionInfo() ? Best, Pierre. > thanks > -s > > >> print(ces); print(ces[1]); > CnChipEffectSet: > Name: AgSNP01_set > Tags: ACC,-XY,BPN,-XY,AVG,A+B > Path: plmData/AgSNP01_set,ACC,-XY,BPN,-XY,AVG,A+B/Ag_SNP_1m520721 > Platform: Affymetrix > Chip type: Ag_SNP_1m520721,monocell > Number of arrays: 81 > Names: EROSE_p_MS_Pop_Struct_Bamako_Ag_SNP_1m520721_A01_458244, > EROSE_p_MS_Pop_Struct_Bamako_Ag_SNP_1m520721_A02_458242, ..., > SAGAS_p_MS_Pop_Pilot1_MM4 > g_SNP_1m520721_D08_445850 > Time period: 2010-02-16 16:39:47 -- 2010-02-16 16:40:00 > Total file size: 1240.10MB > RAM: 0.15MB > Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE, combineAlleles: > logi TRUE) > $Ag_2L_005857148 > $Ag_2L_005857148$AT > $Ag_2L_005857148$AT$theta > [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] > [1,] 40607 49887 58641 74699 73849 59042 57730 44588 56064 53004 47275 43394 > [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] > [1,] 48138 58073 41664 39946 24412 55460 49378 91170 60162 53812 38040 32548 > [,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] > [1,] 4639 6035 63732 62983 70399 8569 10699 56710 63548 40405 49868 33613 > [,37] [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48] > [1,] 44585 20986 33751 49092 43146 42322 38705 30467 31034 23933 54582 32668 > [,49] [,50] [,51] [,52] [,53] [,54] [,55] [,56] [,57] [,58] [,59] > [,60] > [1,] 28798 23453 65232 45382 65549 81326 172111 45896 33892 42695 61220 > 27770 > [,61] [,62] [,63] [,64] [,65] [,66] [,67] [,68] [,69] [,70] [,71] [,72] > [1,] 90138 36600 21338 30336 27390 37789 38993 33366 15584 2688 35110 36887 > [,73] [,74] [,75] [,76] [,77] [,78] [,79] [,80] [,81] > [1,] 39633 37054 47837 47488 48989 36130 35849 20710 33560 > > >> ceR <- getAverageFile(ces, verbose=verbose); > 20100218 13:21:08|Retrieving average cell signals across 81 arrays... > CnChipEffectFile: > Name: .average-intensities-median-mad > Tags: f2e3009e11cbfd8257aa2ba6118e5039 > Full name: .average-intensities-median-mad,f2e3009e11cbfd8257aa2ba6118e5039 > Pathname: > plmData/AgSNP01_set,ACC,-XY,BPN,-XY,AVG,A+B/Ag_SNP_1m520721/.average-intensities-median-mad,f2e3009e11cbfd8257aa2ba6118e5039.CEL > File size: 15.31 MB (16053637 bytes) > RAM: 0.03 MB > File format: v4 (binary; XDA) > Platform: Affymetrix > Chip type: Ag_SNP_1m520721,monocell > Timestamp: 2010-02-16 16:41:57 > Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE, combineAlleles: > logi TRUE) > 20100218 13:21:09|Retrieving average cell signals across 81 arrays...done >> print(ceR); print(ceR[1]); > CnChipEffectFile: > Name: .average-intensities-median-mad > Tags: f2e3009e11cbfd8257aa2ba6118e5039 > Full name: .average-intensities-median-mad,f2e3009e11cbfd8257aa2ba6118e5039 > Pathname: > plmData/AgSNP01_set,ACC,-XY,BPN,-XY,AVG,A+B/Ag_SNP_1m520721/.average-intensities-median-mad,f2e3009e11cbfd8257aa2ba6118e5039.CEL > File size: 15.31 MB (16053637 bytes) > RAM: 0.03 MB > File format: v4 (binary; XDA) > Platform: Affymetrix > Chip type: Ag_SNP_1m520721,monocell > Timestamp: 2010-02-16 16:41:57 > Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE, combineAlleles: > logi TRUE) > $Ag_2L_005857148 > $Ag_2L_005857148$AT > $Ag_2L_005857148$AT$theta > [1] 0 > > > > -- > > Seth Redmond > > Scientific Programmer, VectorBase > > Kafatos / Christophides Groups > > Div. Cell and Molecular Biology > > Imperial College, London > > seth.redm...@imperial.ac.uk > > -- > > -- > 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. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe from this group, send email to > aroma-affymetrix-unsubscr...@googlegroups.com > For more options, visit this group at > http://groups.google.com/group/aroma-affymetrix?hl=en -- 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from th
Re: [aroma.affymetrix] matching affy SNP names with their “rs” names
Hi Max ! Short reply: you can get this information from the NetAffx annotation files. For example, for GenomeWideSNP_6, the mapping can be retrieved from http://www.affymetrix.com/Auth/analysis/downloads/na29/genotyping/GenomeWideSNP_6.na29.annot.csv.zip The first two columns are the SNP id and the rs id. I'll try to add a HowTo on this to the aroma-project.org website soon. Best, Pierre On Wed, Jan 27, 2010 at 5:20 PM, Max Moldovan wrote: > Hi People, > > I am extracting unit names from specific chromosome over specific > region (x,y) e.g.: > > gi <- getGenomeInformation(cdf) > units <- getUnitsOnChromosome(gi, chromosome=2, region=c(x,y)) > unit_names <- getUnitNames(cdf, unit=units) > > “unit_names” will contain something like SNP_A-2243961 and CN_195975 > for SNPs and copy number probes, respectively. > > It is possible to go to a genome browser (e.g. UCSC) and pool “rs” > names for SNPs. > > The question is, can I match the affy names of SNPs (e.g. > SNP_A-2243961) to their “rs” names (i.e. rs17013229) using annotation > information within aroma.affy? > > Thanks and best wishes > > Max > > -- > 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. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe from this group, send email to > aroma-affymetrix-unsubscr...@googlegroups.com > For more options, visit this group at > http://groups.google.com/group/aroma-affymetrix?hl=en > -- 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en
Re: [aroma.affymetrix] basic problem with AffymetrixCelSet
Hi Mike,
Did you try to (g)unzip all your CEL files in
rawData/GSE15907/MoGene-1_0-st-v1 ?
I don't think that aroma.affymetrix can handle gzipped CEL files.
Also, please report your sessionInfo()
Best
Pierre.
On Thu, Jan 28, 2010 at 8:45 AM, mike dewar wrote:
> Hi,
>
> First of all: apologies if I'm missing something obvious.
>
> I'm trying to read a set of CEL files from the ImmGen project,
> (GSE15907). I'm following the document at
> http://groups.google.com/group/aroma-affymetrix/web/gene-1-0-st-array-analysis
> but I'm running into an error I can't interpret. Any help would be
> most appreciated!
>
> My folder structure is the following:
>
> /Users/mike/Data/Immgen
> |-annotationData
> |---chipTypes
> |-MoGene-1_0-st-v1 <--- in here is MoGene-1_0-st-v1,r3.cdf
> |---samples
> |-rawData
> |---GSE15907
> |-MoGene-1_0-st-v1 <--- in here are lots of gzipped CEL
> files
>
> The code I'm using is
>
> library('aroma.affymetrix')
> setwd("/Users/mike/Data/Immgen")
> cdf <- AffymetrixCdfFile$byChipType("MoGene-1_0-st-v1",tags="r3")
> cs <- AffymetrixCelSet$byName("GSE15907",cdf=cdf)
> print(cs)
>
> The error I get is
>
> [2010-01-28 11:41:18] Exception: Argument 'x' is of length 1 although
> the range ([0,0]) implies that is should be empty.
> at throw(Exception(...))
> at throw.default(sprintf("Argument 'x' is of length %d although the
> range ([%s
> at throw(sprintf("Argument 'x' is of length %d although the range
> ([%s,%s]) im
> at getIndices.Arguments(static, ..., length = length)
> at getIndices(static, ..., length = length)
> at method(static, ...)
> at Arguments$getIndex(idx, max = n)
> at getFile.GenericDataFileSet(this, 1)
> at getFile(this, 1)
> at getUnitNamesFile.AffymetrixCelSet(this)
> at getUnitNamesFile(this)
> at getChipType.AffymetrixCelSet(this)
> at getChipType(this)
> at sprintf("Chip type: %s", getChipType(this))
> at as.character.AffymetrixCelSet(x)
> at as.character(x)
> at print(as.character(x))
> at print.Object(cs)
> at print(cs)
> Calls: print ... getIndices.Arguments -> throw -> throw.default ->
> throw -> throw.Exception
> Execution halted
>
> Has anyone got any ideas as to where I'm going wrong?
>
> Cheers,
>
> Mike Dewar
>
> --
> 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.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe from this group, send email to
> aroma-affymetrix-unsubscr...@googlegroups.com
> For more options, visit this group at
> http://groups.google.com/group/aroma-affymetrix?hl=en
>
--
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.
To post to this group, send email to aroma-affymetrix@googlegroups.com
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[aroma.affymetrix] 'affymetrix_calvin_exceptions::FileNotOpenException' [Was: Re: Total CNs analysis]
Hi Anguraj, [cc'ing the mailing list in case other people run into the same problem] I can reproduce the error. Pasting the error message you got in the search box of aroma.affymetrix's discussion page I found this thread http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/13b581ecc47f0b91 which suggests one of the CEL files may be corrupt. Narrowing it down I found that the error does not come from the tumor samples: > csT <- AffymetrixCelSet$byName(dataSet, cdf=cdf, pattern="GSM", > verbose=verbose); > print(csT); AffymetrixCelSet: Name: GSE16619Data Tags: Path: rawData/GSE16619Data/GenomeWideSNP_5 Platform: Affymetrix Chip type: GenomeWideSNP_5,Full,r2 Number of arrays: 119 Names: GSM417171_BC43, GSM417172_BC44, ..., GSM417386_BC161 Time period: 2008-01-16 17:49:01 -- 2008-04-18 22:44:14 Total file size: 5333.27MB RAM: 0.16MB but from the normal samples > csN <- AffymetrixCelSet$byName(dataSet, cdf=cdf, pattern="NA", > verbose=verbose); > print(csN) terminate called after throwing an instance of 'affymetrix_calvin_exceptions::FileNotOpenException' I've had a quick look at the file sizes and they seem correct. I suggest you try the following: 1) store the tumor and normal samples in two different data set directories, named after their GEO ID: rawData/ / GenomeWideSNP_5/ *.CEL / GenomeWideSNP_5/ *.CEL That's what they are: two different data sets. There is no reason to store them in the same folder. 2) Now you can start normalizing the tumor data set without loosing more time. 3) Troubleshoot the problem with the CEL files from the normal data set: I know very little about CEL files but the first lines of the files don't look good, especially the "text/ascii%affymetrix-algorithm-param-" thing and the fact that part of the header seems to be missing: bash-3.00$ head NA06985_Op1_011206_VnV_D10_r1.CEL ;?ffymetrix-calvin-intensity6030075-1192819521-006334-018467-41en-US#%affymetrix-algorithm-param-Percentile75 text/ascii%affymetrix-algorithm-param-CellMargin4 text/ascii&affymetrix-algorithm-param-OutlierHigh1.500 text/ascii%affymetrix-algorithm-param-OutlierLow1.004 text/ascii%affymetrix-algorithm-param-AlgVersion6.0 text/ascii(affymetrix-algorithm-param-FixedCellSizeTRUE text/ascii+affymetrix-algorithm-param-FullFeatureWidth7 text/ascii,affymetrix-algorithm-param-FullFeatureHeight7 text/ascii4affymetrix-algorithm-param-IgnoreOutliersInShiftRowsFALSE text/ascii,affymetrix-algorithm-param-FeatureExtractionTRUE Does this help ? Pierre. On Fri, Jan 15, 2010 at 10:26 AM, Anguraj Sadanandam wrote: > Hi Pierre, > > Sorry to bother you again. > > May be a simple bug, but I am getting this error for the same SNP5 data > analysis. > >> print(cs); > terminate called after throwing an instance of > 'affymetrix_calvin_exceptions::Fi > leNotOpenException' > > I hope you know where to look for the output file. > > THanks, > > Anguraj > -- 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en
Re: [aroma.affymetrix] custom CDF
Hi Zaid, Does your file satisfy the requirements detailed on the corresponding help page ? http://groups.google.com/group/aroma-affymetrix/web/creating-cdf-files-from-scratch Pierre On Wed, Dec 9, 2009 at 4:18 PM, zaid wrote: > Hello, > > I'm trying to create a custom CDF file from a flat file uisng the R > script provided in this group (flat2Cdf()). > > I'm running into errors such as incorrect number of columns, integer > not found etc. > > Is there a standard flat file structure required? Or are there any > flat files available for download? > I just want to try the script and have a standard structure to work > with. > > > Thanks for the help. > > Z > > -- > 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. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe from this group, send email to > aroma-affymetrix-unsubscr...@googlegroups.com > For more options, visit this group at > http://groups.google.com/group/aroma-affymetrix?hl=en > -- 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en
Re: [aroma.affymetrix] GenomeGraphs and BioMart
Hi Maria,
I think you should report this problem to the Bioconductor mailing
list instead, as it has to do with BioMart and GenomeGraphs, not with
aroma.*
Cheers
Pierre.
On Fri, Dec 4, 2009 at 5:14 AM, Maria Traka wrote:
> I am running GenomeGraphs with my exon data and i get the following
> error message. I have used this in the past sucessfully so not sure
> what has changed now...
> Can you help???
> Thanks,
> Maria
>
>> gene<-new("Gene",id="ENSMUSG0047517", type="ensembl_gene_id",
>> biomart=mart)
>
> V1
> 1 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd";>
> 2 EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
> 3
> ERROR: The requested URL could not be retrieved
> 4
> 5
>
> 6
> ERROR
> 7
> The requested URL could not be retrieved
> 8
>
> 9
>
> 10
> While trying to process the request:
> 11
>
> 12
> POST /biomart/martservice? HTTP/1.1
> 13
> Host: www.biomart.org
> 14
> Accept: */*
> 15
> Proxy-Connection: Keep-Alive
> 16
> Content-Length: 680
> 17
> Expect: 100-continue
> 18 Content-Type: multipart/
> form-data; boundary=5c094063af6b
> 19
>
> 20
>
> 21
> The following error was encountered:
> 22
>
> 23
>
> 24
>
> 25
> Invalid Request
> 26
>
> 27
>
> 28
>
> 29 Some
> aspect of the HTTP Request is invalid. Possible problems:
> 30
>
> 31
> Missing or unknown request method
> 32
> Missing URL
> 33
> Missing HTTP Identifier (HTTP/1.0)
> 34
> Request is too large
> 35
> Content-Length missing for POST or PUT requests
> 36
> Illegal character in hostname; underscores are not allowed
> 37
>
> 38 Your cache administrator is HREF="mailto:webm...@bbsrc.ac.uk";>webm...@bbsrc.ac.uk.
> 39
>
> 40
>
> 41
>
> 42 Generated Fri, 04 Dec 2009
> 13:11:25 GMT by BBSRC-wwwcache-service (squid/2.7.STABLE6)
> 43
>
> 44
>
> Error in getBM(c("ensembl_gene_id", "ensembl_transcript_id",
> "ensembl_exon_id", :
> The query to the BioMart webservice returned an invalid result: the
> number of columns in the result table does not equal the number of
> attributes in the query. Please report this to the mailing list.
>
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.
> 1252;LC_MONETARY=English_United Kingdom.
> 1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] grid stats graphics grDevices datasets utils
> methods base
>
> other attached packages:
> [1] RCurl_0.98-1 bitops_1.0-4.1
> GenomeGraphs_1.4.1 biomaRt_2.0.0 limma_2.18.1
> aroma.affymetrix_1.1.0
> [7] aroma.apd_0.1.3 R.huge_0.1.7
> affxparser_1.16.0 aroma.core_1.1.0 aroma.light_1.13.2
> matrixStats_0.1.4
> [13] R.rsp_0.3.4 R.filesets_0.5.1
> digest_0.3.1 R.cache_0.1.7 R.utils_1.1.6
> R.oo_1.4.6
> [19] R.methodsS3_1.0.3 RWinEdt_1.8-1
>
> loaded via a namespace (and not attached):
> [1] XML_2.3-0
>>
>
> --
> 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.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe from this group, send email to
> aroma-affymetrix-unsubscr...@googlegroups.com
> For more options, visit this group at
> http://groups.google.com/group/aroma-affymetrix?hl=en
>
--
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.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe from this group, send email to
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For more options, visit this group at
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Re: [aroma.affymetrix] where is the vignitte for FIRMA?
Hi Wenhong, Here is the Human Exon Array Analysis vignette: http://groups.google.com/group/aroma-affymetrix/web/human-exon-array-analysis It's listed with the other help pages: http://groups.google.com/group/aroma-affymetrix/web Best, Pierre On Fri, Nov 6, 2009 at 4:27 PM, Wenhong wrote: > Hi > Just starting using Aroma.Affymetrix and FIRMA to analyze Exon array. > Can somebody point me the help or vignitte for the packages? Thanks > Wenhong > > -- > 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. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe from this group, send email to > aroma-affymetrix-unsubscr...@googlegroups.com > For more options, visit this group at > http://groups.google.com/group/aroma-affymetrix?hl=en > -- 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en
[aroma.affymetrix] Re: Exception: Unknown arguments: cdf, checkChipType
Hi Carol,
On Mon, Oct 12, 2009 at 9:15 AM, cjb wrote:
>
> Hi all,
>
> I am following along with the Gene 1.0 ST Vignette:
> http://groups.google.com/group/aroma-affymetrix/web/gene-1-0-st-array-analysis
>
> and with Henrik's August 7, 2007 aroma.affymetrix tutorial.
>
> All goes well until I try to do background correction or quantile
> normalization.
>
> When I try to do either background correction or quantile
> normalization I get a similar error:
> Exception: Unknown arguments: cdf, checkChipType
>
> When I look in my working directory, there is a probeData directory
> that has been created. And within that directory, two directories with
> tags.
>
> MGH_Data\probeData\MGH09,QN\MoGene-1_0-st-v1
>
> MGH_Data\probeData\MGH09,RBC\MoGene-1_0-st-v1
>
> 1. Creating the cdf and cs objects:
>
>> cdf <- AffymetrixCdfFile$byChipType("MoGene-1_0-st-v1")
>> cdf
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/MoGene-1_0-st-v1
> Filename: MoGene-1_0-st-v1.cdf
> Filesize: 67.42MB
> Chip type: MoGene-1_0-st-v1
> RAM: 0.00MB
> File format: v3 (text; ASCII)
> Dimension: 1050x1050
> Number of cells: 1102500
> Number of units: 35512
> Cells per unit: 31.05
> Number of QC units: 1
>
>> cs <- AffymetrixCelSet$byName("MGH09",chipType="MoGene-1_0-st-v1")
>> print(cs)
> AffymetrixCelSet:
> Name: MGH09
> Tags:
> Path: rawData/MGH09/MoGene-1_0-st-v1
> Platform: Affymetrix
> Chip type: MoGene-1_0-st-v1
> Number of arrays: 26
> Names: J001_3_11.5, J001_4_11.5, ..., J010_4_16.5
> Time period: 2009-09-23 17:51:49 -- 2009-09-23 21:45:31
> Total file size: 275.06MB
> RAM: 0.02MB
>
Have you tried
cs <- AffymetrixCelSet$byName("MGH09", cdf=cdf)
instead, as in the Gene 1.0 ST Vignette you are citing ?
Also, are you using the latest versions of the packages ? Please give
the output of sessionInfo() so that we can figure this out.
Best,
Pierre.
> 2. RmaBackgroundCorrection(s) Error:
>
>> bc <- RmaBackgroundCorrection(cs)
>> csBC <- process(bc, verbose=verbose)
> Background correcting data set...
>
> Error in list(`process(bc, verbose = verbose)` = ,
> `process.RmaBackgroundCorrection(bc, verbose = verbose)` =
> , :
>
> [2009-10-12 11:49:04] Exception: Unknown arguments: cdf, checkChipType
> at throw(Exception(...))
> at throw.default("Unknown arguments: ", argsStr)
> at throw("Unknown arguments: ", argsStr)
> at GenericDataFileSet(files = files, ...)
> at extend(GenericDataFileSet(files = files, ...),
> "AromaMicroarrayDataSet")
> at AromaMicroarrayDataSet(files = files, ...)
> at extend(AromaMicroarrayDataSet(files = files, ...), c
> ("AffymetrixFileSet", uses("AromaPlatformI
> at AffymetrixFileSet(files = files, ...)
> at extend(AffymetrixFileSet(files = files, ...), "AffymetrixCelSet",
> `cached:.intensities` = NULL
> at this(...)
> at newInstance.Class(clazz, ...)
> at newInstance(clazz, ...)
> at newInstance.Object(static, files, ...)
> at newInstance(static, files, ...)
> at method(static, ...)
> at staticMethod(path = "probeData/MGH09,RBC/MoGene-1_0-st-v1",
> pattern = "^[^.].*[.](CEL|cel)$",
> at do.call("staticMethod", args = args)
> at getOutputDataSet0.AromaTransform(this, ..., verbose
> Background correcting data set...done
>
>
> 3. QuantileNormalization(cs) Error:
>
>> qn <-QuantileNormalization(cs)
>> qn
> Error in list(`print(NA)` = , `print.Object(NA)` =
> , :
>
> [2009-10-12 11:33:42] Exception: Unknown arguments: cdf, checkChipType
> at throw(Exception(...))
> at throw.default("Unknown arguments: ", argsStr)
> at throw("Unknown arguments: ", argsStr)
> at GenericDataFileSet(files = files, ...)
> at extend(GenericDataFileSet(files = files, ...),
> "AromaMicroarrayDataSet")
> at AromaMicroarrayDataSet(files = files, ...)
> at extend(AromaMicroarrayDataSet(files = files, ...), c
> ("AffymetrixFileSet", u
> at AffymetrixFileSet(files = files, ...)
> at extend(AffymetrixFileSet(files = files, ...), "AffymetrixCelSet",
> `cached:.
> at this(...)
> at newInstance.Class(clazz, ...)
> at newInstance(clazz, ...)
> at newInstance.Object(static, files, ...)
> at newInstance(static, files, ...)
> at method(static, ...)
> at staticMethod(path = "probeData/MGH09,QN/MoGene-1_0-st-v1",
> pattern = "^[^.]
> at do.call("staticMethod", args = args)
>
>
> >
>
--~--~-~--~~~---~--~~
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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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-~--~~~~--~~--~--~---
[aroma.affymetrix] Re: Correspondence between aroma alleles and affy annotation
Hi, On Wed, Sep 16, 2009 at 2:43 AM, marco wrote: > > Hi Pierre, > > I am following the CRMA2 vignette, so I am using the > GenomeWideSNP_6,Full.cdf. > At the same time I extracted the Allele A and B from the .csv > annotation file provided by affy (GenomeWideSNP_6.na26.annot.csv) FYI: the current version on NetAffx website is GenomeWideSNP_6.na29.annot.csv, see http://www.affymetrix.com/products_services/arrays/specific/genome_wide_snp6/genome_wide_snp_6.affx#1_4 > I guess that the .cdf and the .csv match. Not really, as strange as it can sound; see below. > So my question is if the alleleB of aroma is the allele B of affy. Is > that the case ? > Yes, it is: aroma.affymetrix uses allele definitions of the cdf you are working with, and you are working with Affy's cdf. To answer your original question, which I think I've now understood: you want to use the "strand" information, which is also in NetAffx files: whenever the strand is "-" you have to swap what the cdf (or aroma.affymetrix) calls allele A and allele B to make it consistent with the allele A and allele B definition in the netAffx file. If you don't do this, then the allele definition of the cdf does not match that of NetAffx (even if you take the "direction" information from the cdf into account, but that's another story). It took me quite a while to figure this out when I first had to. I hope this will help you. Best, Pierre. > > thanks a lot for the help! > > Best Regards > > Marco > > > On Sep 16, 6:56 am, Pierre Neuvial wrote: >> Hi Marco, >> >> In case you haven't solved your problem yet... >> >> I think they should be the same if you have analyzed your data using >> one of the CDF provided by Affymetrix, which is most likely. >> What are you calling "the affy annotation file for the SNP6.0" ? What >> CDF have you used ? >> >> Best, >> >> Pierre. >> >> On Mon, Sep 7, 2009 at 1:47 AM, marco wrote: >> >> > Dear Henrik, >> >> > is there a correspondence between what in Aroma is called "ALLELE >> > B" (for example in extractTotalAndFreqB) and the "ALLELE B" in the >> > affy annotation file for the SNP6.0 ? >> >> > I would like to compare the caucasian frequencies as declared by affy >> > with the frequencies estimated by pooling a ctrl cohort but it seems >> > to me that the two "B" do not correspond to each other. Is there any >> > way to correspond the alleles? >> >> > Best Regards >> >> > Marco > > > --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: Correspondence between aroma alleles and affy annotation
Hi Marco, In case you haven't solved your problem yet... I think they should be the same if you have analyzed your data using one of the CDF provided by Affymetrix, which is most likely. What are you calling "the affy annotation file for the SNP6.0" ? What CDF have you used ? Best, Pierre. On Mon, Sep 7, 2009 at 1:47 AM, marco wrote: > > Dear Henrik, > > is there a correspondence between what in Aroma is called "ALLELE > B" (for example in extractTotalAndFreqB) and the "ALLELE B" in the > affy annotation file for the SNP6.0 ? > > I would like to compare the caucasian frequencies as declared by affy > with the frequencies estimated by pooling a ctrl cohort but it seems > to me that the two "B" do not correspond to each other. Is there any > way to correspond the alleles? > > > Best Regards > > Marco > > > > --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: array names
Hi,
Try using getNames, e.g.
getNames(cesN)
Cheers,
Pierre.
On Fri, Sep 11, 2009 at 8:26 AM, mbaudis wrote:
>
> Dear all,
>
> how can I access a vector containing all array names used during
> processing?
>
> Also, can one run the segmentation not by chromosome, but by array (or
> specify both)? I could extract the names from the regions file after
> segmentation
>
> levels(names(reg))
>
> but would miss out on arrays without changes CNVs, and also want to
> have the names before segmentation.
>
> Currently, I run:
>
> for(i in 1:23) {
> cbs <- CbsModel(cesN, cesCRef)
> reg <- getRegions(cbs, chromosomes=i, verbose=verbose)
> for(i in 1:length(names(reg))) {
> segtable <- reg[names(reg)[[i]]][[1]][,1:5]
> segtable <- cbind(rep(names(reg)[i], length(segtable[,1])),
> segtable)
> write.table(segtable, file = segmentsfile, append = TRUE,
> col.names
> = FALSE, row.names = FALSE, quote = FALSE, sep = "\t")
> }
> }
>
>
> 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
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-~--~~~~--~~--~--~---
[aroma.affymetrix] Re: copy number calls in the output
Hi Suresh, The answer is no as CBS is just a segmentation method, not a segmentation and calling method as GLAD is. So what you can compare between the two is just the output of the segmentation. FYI there is also a wrapper for HaarSeg (also segmentation only) in aroma.affymetrix, in case you'd like to give it a try. E. Ben-Yaacov and Y. C. Eldar. A fast and flexible method for the segmentation of aCGH data. Bioin- formatics, 24(16):i139–i145, Aug 2008. Cheers, Pierre. On Fri, Aug 21, 2009 at 4:23 AM, ssv wrote: > > Hi Henrik > > Here is another question. I was trying to compare ouput from cbs model > with that from glad model. After processing, (.tsv) xls files are > created in respective directories. While xls (.tsv) file for glad > model has copy number calls written to the file (neutral, gain and > loss), cbs file doesn't have it. Can this variable be written to the > tsv file for CBS model too ? > > Isuresh > > > --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: Log2 data
Hi David,
First a comment on your previous post: I understand you've been using
of the code of the Total copy number vignette
http://groups.google.com/group/aroma-affymetrix/web/total-copy-number-analysis
in which quantile normalization is used. If you read between the code
lines, you will see the following comment:
"Comment: In Bengtsson et al. (2008), we show that it is better to do
allelic-crosstalk calibration and use quantile normalization as an
optional follow-up step. However, since this example was prepared
before those results we concluded, we here only show how to perform
the quantile normalization. Please see other vignette for the GWS6
chip type to see how to do allelic-crosstalk calibration."
This means replacing:
qn <- QuantileNormalization(cs)
csN <- process(qn, verbose=log)
by:
acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
csC <- process(acc, verbose=log)
bpn <- BasePositionNormalization(csC, target="zero")
csN <- process(bpn, verbose=log)
FYI this page gives you the last version of the normalization and
summarization steps:
http://groups.google.com/group/aroma-affymetrix/web/code-snippets
In short, there are (at least) two good reasons for doing this:
1. you will be correcting the "cause" rather than the "symptom"
(sounds like Henrik is talking...).
2. it makes this step a single array step, which is a good point for
the discussion below.
See the CRMAv1 and v2 papers for more details:
Bengtsson, H.; Irizarry, R. A.; Carvalho, B. & Speed, T. P. Estimation
and assessment of raw copy numbers at the single locus level.
Bioinformatics, 2008, 24, 759-767. (CRMA v1 paper)
http://bioinformatics.oxfordjournals.org/cgi/content/full/24/6/759
Bengtsson, H.; Wirapati, P. & Speed, T. P. A single-array
preprocessing method for estimating full-resolution raw copy numbers
from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6.
Bioinformatics, 2009 (accepted). (CRMA v2 paper)
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp371v1
See below for a reply to your question.
On Wed, Aug 12, 2009 at 7:02 PM, David wrote:
>
> Thanks for the replay Pierre!
>
> I have the following:
> 27 tumors
> 38 Controls
>
> And I wonder the appropiate proccess design:
>
> Should I analize at the sametime, controls and tumors?
>
> or should I analize them individually? first, the set of tumors and
> then the set of controls.
>
> Finally, in order to obtain the log2ratio and considering both sets,
> what could be the best?
My short answer is you should analyze them all at the same time. By
"analyze" I mean "normalize and summarize".
FYI: In the code you have posted there are two multi array steps:
quantile normalization and RMA summarization. Note that if you follow
the CRMAv2 snippet for 10-500K (at
http://groups.google.com/group/aroma-affymetrix/web/code-snippets) as
I've suggested above then the only multi-array step is the RMA
summarization.
At this stage I strongly suggest that you check what the densities of
signal intensities look like before and after normalization, using
'plotDensity'.
For the segmentation, assuming that cesNList is a list of two chip
types with 27+38 arrays in each, you can split them into one list for
tumors and one list for controls:
cesNListT <- lapply(cesNList, extract, 1:27) ## assuming the first 27 are tumors
cesNListC <- lapply(cesNList, extract, 27+1:38) ## assuming the last
27 are controls
and define your GladModel as
glad <- GladModel(cesNListT, cesNListC) ## add all your favorite
options for GLAD here
This way cesNListC will be averaged to build a "reference array" Then
you can proceed as before and this reference array will be used to
calculate log-ratios and perform segmentation.
Cheers,
Pierre.
>
> Thanks again!
>
> David
>
> On Aug 11, 9:22 am, Pierre Neuvial wrote:
>> Hi David,
>>
>> Your code seems to be correct, but see remarks below.
>>
>>
>>
>> On Fri, Jul 24, 2009 at 6:39 PM, David wrote:
>>
>> > Hi, to everyone!
>>
>> > I working with a set of 27 Cervican Cancer tumors using Affy 100k. I
>> > would like to get the log2 value for each SNP.
>>
>> > I´m running the vignette (Everything runs just fine):
>>
>> > library(aroma.affymetrix)
>> > verbose <- Arguments$getVerbose(-8)
>> > timestampOn(verbose)
>> > name <- "oscar"
>> > chipTypes <- c("Mapping50K_Hind240", "Mapping50K_Xba240")
>> > cdfs <- lapply(chipTypes, FUN=function(chipType) { AffymetrixCdfFile
>> > $byChipType(chipType) })
>> > print(cdfs)
>> > gis <- lapply(cdfs, getGenomeInformation)
>> > print(gis
[aroma.affymetrix] Re: Log2 data
Hi David,
Your code seems to be correct, but see remarks below.
On Fri, Jul 24, 2009 at 6:39 PM, David wrote:
>
> Hi, to everyone!
>
> I working with a set of 27 Cervican Cancer tumors using Affy 100k. I
> would like to get the log2 value for each SNP.
>
> I´m running the vignette (Everything runs just fine):
>
> library(aroma.affymetrix)
> verbose <- Arguments$getVerbose(-8)
> timestampOn(verbose)
> name <- "oscar"
> chipTypes <- c("Mapping50K_Hind240", "Mapping50K_Xba240")
> cdfs <- lapply(chipTypes, FUN=function(chipType) { AffymetrixCdfFile
> $byChipType(chipType) })
> print(cdfs)
> gis <- lapply(cdfs, getGenomeInformation)
> print(gis)
> sis <- lapply(cdfs, getSnpInformation)
> print(sis)
> cesNList <- list()
>
> chipType <- chipTypes[1]
> cs <- AffymetrixCelSet$byName(name, chipType=chipType)
> cs <- extract(cs, !isDuplicated(cs))
> print(cs)
> qn <- QuantileNormalization(cs)
> print(qn)
> csN <- process(qn, verbose=-20)
> plm <- RmaCnPlm(csN, combineAlleles=TRUE, mergeStrands=TRUE)
> print(plm)
> fit(plm, verbose=-20)
> ces <- getChipEffectSet(plm)
> fln <- FragmentLengthNormalization(ces)
> print(fln)
> cesNList[[chipType]] <- process(fln, verbose=verbose)
>
> chipType <- chipTypes[2]
> cs <- AffymetrixCelSet$byName(name, chipType=chipType)
> cs <- extract(cs, !isDuplicated(cs))
> print(cs)
> qn <- QuantileNormalization(cs)
> print(qn)
> csN <- process(qn, verbose=-20)
> plm <- RmaCnPlm(csN, combineAlleles=TRUE, mergeStrands=TRUE)
> print(plm)
> fit(plm, verbose=-20)
> ces <- getChipEffectSet(plm)
> fln <- FragmentLengthNormalization(ces)
> print(fln)
> cesNList[[chipType]] <- process(fln, verbose=verbose)
>
>
> glad <- GladModel(cesNList, mediancenter = FALSE, smoothfunc =
> "lawsglad", bandwidth = 10, round = 1.5, model = "Gaussian", lkern =
> "Exponential", qlambda = 0.999, base = FALSE, lambdabreak = 8,
> lambdacluster = 8, lambdaclusterGen = 40, type = "tricubic", param = c
> (d = 100), alpha = 0.001, msize = 5, method = "centroid", nmax = 8,
> verbose = FALSE)
> fit(glad, chromosomes=1:23, verbose=verbose)
> writeRegions(glad, chromosomes=1:23, verbose=verbose)
>
Note that if you are interested in the raw copy numbers (ie the values
after normalization) then you don't need the last two lines: you can
just call
extractRawCopyNumbers(glad)
without having fit the segmentation model (which makes sense because
these are raw copy numbers, so segmentation is not needed to get
them). And for the same reason the raw copy numbers will be the same
if you were using other parameters for GladModel, or even if you were
using CbsModel (or HaarSegModel) instead.
> #from this point I´m a little lost
> dataName <- getNames( glad )
> for( j in 1:27 ) {
> df<-NULL
> for ( i in 1:23 ) {
> rawCNs <- extractRawCopyNumbers(glad, array=j, chromosome=i);
> print(rawCNs);
> rawCNs <- as.data.frame(rawCNs);
> str(rawCNs);
> v<-c(i);
> df2<-data.frame(cbind(rawCNs, chr=rep(v,dim(rawCNs)[1])));
> df<-rbind(df,df2)
> }
> nam <- paste( dataName[j] , j, ".txt", sep="" )
> write.table(df, nam , quote = FALSE, sep = '\t',row.names =
> FALSE,col.names = TRUE);
> }
>
> How could I calculate the log2 data?
In theory the above loop does what you expect and gives you log2ratios
(relative to a reference defined for each SNP as a robust average (ie
median) of the signal intensities of all chips). However as you have
probably experienced the data.frame you will be creating a huge
data.frame, and doing cbind at each step will be slower and slower,
until you run out of memory.
As far as I understand, this is why extractRawCopyNumbers only
supports one array and one chromosome at a time.
The best option for you depends on what you want to do with your data
afterwards. Do you really need all your data in a big text file ?
Hope this helps,
Pierre.
>
> is there any documentation to extractRawCopyNumbers?
>
>
>
> Thanks in advance!
>
> David
>
> >
>
--~--~-~--~~~---~--~~
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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-~--~~~~--~~--~--~---
[aroma.affymetrix] Re: Exception: The fit function for requested RMA PLM flavor failed: affyPLM
Hi Mark,
It works as expected now. Thanks a lot for you extra-quick reply.
Pierre
On Thu, Aug 6, 2009 at 11:27 PM, Mark Robinson wrote:
>
> Hi Pierre.
>
> It looks like your version of 'preprocessCore' is VERY outdated.
> Version 1.6.0 is the one that should go with 2.9.x (BioC 2.4) and you
> have 1.0.0 ...
>
> Cheers,
> Mark
>
>
> On 07/08/2009, at 7:23 AM, Pierre Neuvial wrote:
>
>>
>> Hi,
>>
>> I'm having trouble analyzing a set of 250K SNP arrays using the CRMAv2
>> code from http://groups.google.com/group/aroma-affymetrix/web/code-snippets
>> :
>> I've got an error at the summarization step:
>>
>>> plm <- RmaCnPlm(csN, mergeStrands=TRUE, combineAlleles=TRUE)
>>> fit(plm, verbose=log)
>>
>> 20090806 12:42:04| Identifying non-fitted units in chip-effect
>> file...done
>> 20090806 12:42:04| Identifying non-estimated units...done
>> 20090806 12:42:04| Getting model fit for 262338 units.
>> Loading required package: preprocessCore
>> > 'list', not a 'character'>
>> Error in list(`source("R/CRMAv2.R")` = ,
>> `eval.with.vis(ei, envir)` = , :
>>
>> [2009-08-06 12:42:04] Exception: The fit function for requested RMA
>> PLM flavor failed: affyPLM
>> at throw(Exception(...))
>> at throw.default("The fit function for requested RMA PLM flavor
>> failed: ", fla
>> at throw("The fit function for requested RMA PLM flavor failed: ",
>> flavor)
>> at getFitUnitGroupFunction.RmaPlm(this, ...)
>> at getFitUnitGroupFunction(this, ...)
>> at getFitUnitFunction.CnPlm(this)
>> at getFitUnitFunction(this)
>> at fit.ProbeLevelModel(plm, verbose = log)
>> at fit(plm, verbose = log)
>> at eval.with.vis(expr, envir, enclos)
>> at eval.with.vis(ei, envir)
>> at source("R/CRMAv2.R")
>> 20090806 12:42:04|Fitting model of class RmaCnPlm:...done
>>
>> From previous discussions on the list I understand this could come
>> from recent modifications to preprocessCore.
>> It could also come from the fact that I am using R 2.9.0 and cannot
>> switch to R 2.9.1 quickly right now.
>>
>> Cheers,
>>
>> Pierre.
>>
>>> traceback()
>> 13: throw.Exception(Exception(...))
>> 12: throw(Exception(...))
>> 11: throw.default("The fit function for requested RMA PLM flavor
>> failed: ",
>> flavor)
>> 10: throw("The fit function for requested RMA PLM flavor failed: ",
>> flavor)
>> 9: getFitUnitGroupFunction.RmaPlm(this, ...)
>> 8: getFitUnitGroupFunction(this, ...)
>> 7: getFitUnitFunction.CnPlm(this)
>> 6: getFitUnitFunction(this)
>> 5: fit.ProbeLevelModel(plm, verbose = log)
>> 4: fit(plm, verbose = log)
>> 3: eval.with.vis(expr, envir, enclos)
>> 2: eval.with.vis(ei, envir)
>> 1: source("R/CRMAv2.R")
>>> sessionInfo()
>> R version 2.9.0 (2009-04-17)
>> x86_64-redhat-linux-gnu
>>
>> locale:
>> LC_CTYPE
>> =
>> en_US
>> .UTF
>> -8
>> ;LC_NUMERIC
>> =
>> C
>> ;LC_TIME
>> =
>> en_US
>> .UTF
>> -8
>> ;LC_COLLATE
>> =
>> en_US
>> .UTF
>> -8
>> ;LC_MONETARY
>> =
>> C
>> ;LC_MESSAGES
>> =
>> en_US
>> .UTF
>> -8
>> ;LC_PAPER
>> =
>> en_US
>> .UTF
>> -8
>> ;LC_NAME
>> =
>> C
>> ;LC_ADDRESS
>> =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] preprocessCore_1.0.0 aroma.affymetrix_1.1.0 aroma.apd_0.1.6
>> [4] R.huge_0.1.8 affxparser_1.16.0 aroma.core_1.1.2
>> [7] aroma.light_1.12.2 matrixStats_0.1.6 R.rsp_0.3.4
>> [10] R.filesets_0.5.2 digest_0.3.1 R.cache_0.1.7
>> [13] R.utils_1.1.7 R.oo_1.4.8 R.methodsS3_1.0.3
>>>
>>
>> >
>
> --
> Mark Robinson, PhD (Melb)
> Epigenetics Laboratory, Garvan
> Bioinformatics Division, WEHI
> e: m.robin...@garvan.org.au
> e: mrobin...@wehi.edu.au
> p: +61 (0)3 9345 2628
> f: +61 (0)3 9347 0852
> --
>
>
>
>
>
>
> >
>
--~--~-~--~~~---~--~~
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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-~--~~~~--~~--~--~---
[aroma.affymetrix] Exception: The fit function for requested RMA PLM flavor failed: affyPLM
Hi,
I'm having trouble analyzing a set of 250K SNP arrays using the CRMAv2
code from http://groups.google.com/group/aroma-affymetrix/web/code-snippets:
I've got an error at the summarization step:
> plm <- RmaCnPlm(csN, mergeStrands=TRUE, combineAlleles=TRUE)
> fit(plm, verbose=log)
20090806 12:42:04| Identifying non-fitted units in chip-effect file...done
20090806 12:42:04| Identifying non-estimated units...done
20090806 12:42:04| Getting model fit for 262338 units.
Loading required package: preprocessCore
Error in list(`source("R/CRMAv2.R")` = ,
`eval.with.vis(ei, envir)` = , :
[2009-08-06 12:42:04] Exception: The fit function for requested RMA
PLM flavor failed: affyPLM
at throw(Exception(...))
at throw.default("The fit function for requested RMA PLM flavor failed: ", fla
at throw("The fit function for requested RMA PLM flavor failed: ", flavor)
at getFitUnitGroupFunction.RmaPlm(this, ...)
at getFitUnitGroupFunction(this, ...)
at getFitUnitFunction.CnPlm(this)
at getFitUnitFunction(this)
at fit.ProbeLevelModel(plm, verbose = log)
at fit(plm, verbose = log)
at eval.with.vis(expr, envir, enclos)
at eval.with.vis(ei, envir)
at source("R/CRMAv2.R")
20090806 12:42:04|Fitting model of class RmaCnPlm:...done
>From previous discussions on the list I understand this could come
from recent modifications to preprocessCore.
It could also come from the fact that I am using R 2.9.0 and cannot
switch to R 2.9.1 quickly right now.
Cheers,
Pierre.
> traceback()
13: throw.Exception(Exception(...))
12: throw(Exception(...))
11: throw.default("The fit function for requested RMA PLM flavor failed: ",
flavor)
10: throw("The fit function for requested RMA PLM flavor failed: ",
flavor)
9: getFitUnitGroupFunction.RmaPlm(this, ...)
8: getFitUnitGroupFunction(this, ...)
7: getFitUnitFunction.CnPlm(this)
6: getFitUnitFunction(this)
5: fit.ProbeLevelModel(plm, verbose = log)
4: fit(plm, verbose = log)
3: eval.with.vis(expr, envir, enclos)
2: eval.with.vis(ei, envir)
1: source("R/CRMAv2.R")
> sessionInfo()
R version 2.9.0 (2009-04-17)
x86_64-redhat-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] preprocessCore_1.0.0 aroma.affymetrix_1.1.0 aroma.apd_0.1.6
[4] R.huge_0.1.8 affxparser_1.16.0 aroma.core_1.1.2
[7] aroma.light_1.12.2 matrixStats_0.1.6 R.rsp_0.3.4
[10] R.filesets_0.5.2 digest_0.3.1 R.cache_0.1.7
[13] R.utils_1.1.7 R.oo_1.4.8 R.methodsS3_1.0.3
>
--~--~-~--~~~---~--~~
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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-~--~~~~--~~--~--~---
[aroma.affymetrix] Re: Warnings after installation
Hi Peng, Can you report the output of sessionInfo() and post the complete code you have run before you got these warnings ? It is hard (for me at least) to figure out what happened if I don't know what you did and in which environment. Cheers, Pierre. On Tue, Aug 4, 2009 at 10:28 PM, Peng Yu wrote: > > Hi, > > I see the following warnings after I installed aroma.affymetrix. I am > wondering whether I need to something to fix the warnings. > > Regards, > Peng > >> warnings() > Warning messages: > 1: In install.packages(pkgs = "aroma.apd", type = "source", ... : > installation of package 'aroma.apd' had non-zero exit status > 2: In install.packages(pkgs = "aroma.core", type = "source", ... : > installation of package 'aroma.core' had non-zero exit status > 3: In packageDescription(pkg) : no package 'aroma.light' was found > 4: In packageDescription(pkg) : no package 'affxparser' was found > 5: In safeSource() : Redefining \u2018biocinstall\u2019 > 6: In safeSource() : Redefining \u2018biocinstallPkgGroups\u2019 > 7: In safeSource() : Redefining \u2018biocinstallRepos\u2019 > 8: In packageDescription(pkg) : no package 'DNAcopy' was found > 9: In safeSource() : Redefining \u2018biocinstall\u2019 > 10: In safeSource() : Redefining \u2018biocinstallPkgGroups\u2019 > 11: In safeSource() : Redefining \u2018biocinstallRepos\u2019 > 12: In packageDescription(pkg) : no package 'GLAD' was found > 13: In safeSource() : Redefining \u2018biocinstall\u2019 > 14: In safeSource() : Redefining \u2018biocinstallPkgGroups\u2019 > 15: In safeSource() : Redefining \u2018biocinstallRepos\u2019 > 16: In library(package, lib.loc = lib.loc, character.only = > TRUE, ... : > there is no package called 'aroma.core' > 17: In library(package, lib.loc = lib.loc, character.only = > TRUE, ... : > there is no package called 'aroma.affymetrix' > > > > --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: Copy numbers using CBS
Hi Suman, You can also use writeRegions directly, as in: writeRegions(cbs, chromosomes=22, verbose=verbose) This won't generate the ChromosomeExplorer report as in the code in my previous post, but it will create the .xls file with copy number regions. Cheers, Pierre. On Sat, Jul 25, 2009 at 7:28 PM, Pierre Neuvial wrote: > Hi Suman, > > I think the easiest way to get the segmentation results into a text > file is to use the code at the bottom of the Total Copy Number > analysis vignette: > > http://groups.google.com/group/aroma-affymetrix/web/total-copy-number-analysis-6-0 > > Specifically, if cesN is your CnChipEffectSet, you can do: > > cbs <- CbsModel(cesN) > ce <- ChromosomeExplorer(cbs) > process(ce, chromosomes=22, verbose=verbose) > > (here I'm using 'chromosomes=22' to do a quick analysis of this > chromosome only but you can analyze several or all of them at the same > time.) This will create not only the .xdr files you mentioned but also > a '.xls' file in the folder cbsData//, that > contains the segmentation results. > > Note that this file is actually a tab delimited text file, although > its extension is .xls (so that it can be opened by Excel directly). > > Hope this helps, > > Pierre. > > FYI, .xdr files are binary files that you can load using 'loadObject'. > > On Fri, Jul 24, 2009 at 5:27 PM, Suman wrote: >> >> I used the fit() function now to output the segmentation output to >> cbsData folder. The output files are in .xdr format. Is there a way to >> convert them to text format or read them back in using R? >> >> On Jul 23, 3:50 pm, Suman wrote: >>> Hi, >>> >>> I used the cbsmodel() function to perform the cbs on the 250k chip >>> array data >>> >>> cbs<-cbsModel(cesN) >>> >>> How do I write the segmentation results to a text file? Is there an >>> underlying function? >>> >>> Any pointers will be helpful >>> >>> Thanks, >>> Suman >> >> >> > --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: Copy numbers using CBS
Hi Suman, I think the easiest way to get the segmentation results into a text file is to use the code at the bottom of the Total Copy Number analysis vignette: http://groups.google.com/group/aroma-affymetrix/web/total-copy-number-analysis-6-0 Specifically, if cesN is your CnChipEffectSet, you can do: cbs <- CbsModel(cesN) ce <- ChromosomeExplorer(cbs) process(ce, chromosomes=22, verbose=verbose) (here I'm using 'chromosomes=22' to do a quick analysis of this chromosome only but you can analyze several or all of them at the same time.) This will create not only the .xdr files you mentioned but also a '.xls' file in the folder cbsData//, that contains the segmentation results. Note that this file is actually a tab delimited text file, although its extension is .xls (so that it can be opened by Excel directly). Hope this helps, Pierre. FYI, .xdr files are binary files that you can load using 'loadObject'. On Fri, Jul 24, 2009 at 5:27 PM, Suman wrote: > > I used the fit() function now to output the segmentation output to > cbsData folder. The output files are in .xdr format. Is there a way to > convert them to text format or read them back in using R? > > On Jul 23, 3:50 pm, Suman wrote: >> Hi, >> >> I used the cbsmodel() function to perform the cbs on the 250k chip >> array data >> >> cbs<-cbsModel(cesN) >> >> How do I write the segmentation results to a text file? Is there an >> underlying function? >> >> Any pointers will be helpful >> >> Thanks, >> Suman > > > --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: cRMA v2
Hi "ZZ",
First, could you please sign with an explicit name (and possibly
affiliation) or write using an explicit email address ? I (we) think
that's the least that can be expected from someone asking for advice
from this group.
You'll find an answer to the second part of your question below.
On Thu, Jul 23, 2009 at 6:11 PM, ZZ wrote:
>
> Hi,
>
> I'm trying to do some copy number analysis of SNP6 data with
> aroma.affymetrix package. I followed the instructions for cRMA v2
> (followed by CBS segmentation). The codes ran smoothly except for the
> occasional appearance of the following message: (regexpr(pattern, header$identifier) == -1) { throw("Rcache file
> format error ('", pathname, "'). Invalid identifier: ", header
> $identifier)}: argument is of length zero>
>
> However, the resulting regions.xls file look rather
> strange as it essentially contains the entire genome instead of a list
> of regions with CN change. Am I missing something here? Your advice
> will be greatly appreciated!
>
The output you have pasted is a list of all regions between CN
breakpoints (and their associated mean signal value) as detected by
CBS on chromosome 1 in your sample. 23 breakpoints have been detected
by CBS, hence 24 regions are reported. This is the output of a
segmentation algorithm, not a calling algorithm, so it does not claim
that some regions are "normal" and other have "CN changes".
You can see what the results look like using the ChromosomeExplorer by calling
display(ce)
This type of output is not specific to CBS: you would obtain the same
type of output (but not exactly the same regions) if you had used GLAD
or HaarSeg for the segmentation (using GladModel or HaarSegModel
instead of CbsModel).
Hope this helps,
Pierre.
> Thank you so much,
>
> ZZ
>
> results from regions.xls file (for chromosome 1 and one of the
> samples):
>
> chromosome start stop mean
> 1 51599 16024215 0.044
> 1 16026085 16026513 -1.597
> 1 16026789 65603493 0.028
> 1 65604012 101989769 -0.028
> 1 101992806 107546773 -0.089
> 1 107551303 108227165 -0.035
> 1 108227977 72261 0.02
> 1 75616 85496 -0.215
> 1 89708 117478252 0.019
> 1 117480483 146842186 -0.01
> 1 146851962 147523316 -0.242
> 1 147526041 152059582 -0.004
> 1 152062361 155683396 0.036
> 1 155687575 167483561 -0.014
> 1 167500599 167505369 -1.075
> 1 167508391 171552881 -0.039
> 1 171555366 184106698 -0.005
> 1 184107922 198087432 -0.089
> 1 198087435 221395875 -0.007
> 1 221395906 223280177 0.018
> 1 223283888 223459246 -0.103
> 1 223459312 227877793 0.022
> 1 227883480 227886820 -2.806
> 1 227887054 247191012 0.001
>
> library("aroma.affymetrix")
> log <- Arguments$getVerbose(-8, timestamp=TRUE)
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
> csR <- AffymetrixCelSet$byName("testSet", cdf=cdf)
> acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
> csC <- process(acc, verbose=log)
> bpn <- BasePositionNormalization(csC, target="zero")
> csN <- process(bpn, verbose=log)
> plm <- AvgCnPlm(csN, mergeStrands=TRUE, combineAlleles=TRUE)
> fitCnProbes(plm, verbose=log)
> fit(plm, verbose=log)
> ces <- getChipEffectSet(plm)
> fln <- FragmentLengthNormalization(ces, target="zero")
> cesN <- process(fln, verbose=log)
> cbs <- CbsModel(cesN)
> ce <- ChromosomeExplorer(cbs)
> process(ce,chromosomes=c(1),verbose=log)
>
>> sessionInfo()
> R version 2.9.1 (2009-06-26)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;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.affymetrix_1.1.1 aroma.apd_0.1.6 affxparser_1.16.0
> [4] R.huge_0.1.8 aroma.core_1.1.2 aroma.light_1.12.2
> [7] matrixStats_0.1.6 R.rsp_0.3.4 R.filesets_0.5.2
> [10] digest_0.3.1 R.cache_0.1.7 R.utils_1.1.7
> [13] R.oo_1.4.8 R.methodsS3_1.0.3
>
>
>
>
> >
>
--~--~-~--~~~---~--~~
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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T
[aroma.affymetrix] Re: segmentation file without ChromosomeExplorer
Hi Michael, On Tue, Jun 9, 2009 at 3:22 AM, mbaudis wrote: > > Dear all, > > how can one generate the segmentation file (& modify it's format) > without plotting images via ChromosomeExplorer? I have written my own > method, and don't need the wast of processing time and space. Also, > this would allow to get rid of the EBImage dependency (?). > > Currently, I do > >>cbs <- CbsModel(cesN, ceSexRef) >>fit(cbs, chromosomes=1:23, verbose=verbose) >>ce <- ChromosomeExplorer(cbs) >>process(ce, chromosomes=1:23, zooms=c(8), verbose=verbose) > > The "fit (cbs...)" step alone will not write out the segmentation. At > least one zoom level is required here. You don't need the last two lines. The fit step does write the segmentation to file (in cbsData/[,paired]/). In order to retrieve the copy number regions you can do reg <- getRegions(cbs) Notes: - you can fit only a subset of chromosomes and/or arrays using 'chromosomes' and 'arrays' arguments of 'fit'. Same for 'getRegions'. - if some arrays or chromosomes in your "cbs" object have not been fitted yet when you call 'getRegions', they will be fitted (and written to disc) Hope this helps, Pierre. > > Thanks fo rcomments, > > Michael. > www.progenetix.net > > > --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: defining cell files
OK, I meant the other way round: the name of the folder should be
rawData/CLP/GenomeWideSNP_6
not
rawData/CLP/GenomeWideSNP_6.0
Best,
Pierre.
On Thu, Jun 4, 2009 at 6:36 AM, Pierre Neuvial wrote:
> Hi Myriam,
>
> On Thu, Jun 4, 2009 at 4:38 AM, Myriam wrote:
>>
>> Hi,
>>
>> I have done (and seems OK, no error message) the low level analysis of
>> the GenomeWideSNP_6.0 for preparing the analysis of my Affymetrix
>> results in 50 samples.
>> However, I cannot get through the steps of defining the CEL files set.
>> I have put all the CEL files in rawData/CLP/GenomeWideSNP_6.0 folder.
>> How should I define the set of CEL files to be analysed and which are
>> contained in that subfolder?
>> Tried command:
>> cs <- AffymetrixCelSet$byName("CLP", cdf=cdf)
>> but error: AffymetrixCelSet not found
>
> The name of the folder containing the CEL files should match the name
> of the chip type exactly. In your case it should be
>
> rawData/CLP/GenomeWideSNP_6.0
>
> not
>
> rawData/CLP/GenomeWideSNP_6
>
> Does this work now ?
>
> For future posts: it's better to give the complete R output; In your
> case aroma.affymetrix probably reports something like:
>
> Cannot create AffymetrixCelSet. *No such directory: CLP/GenomeWideSNP_6*
>
> which tells you (and us) where the problem comes from.
>
> Best,
>
> Pierre
>
>>
>> I am a bit lost, as a beginner. Sorry to bother but hopefully one of
>> you can help me?
>>
>> Thanks in advance,
>> Myriam
>>
>> >>
>>
>
--~--~-~--~~~---~--~~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
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-~--~~~~--~~--~--~---
[aroma.affymetrix] Re: defining cell files
Hi Myriam,
On Thu, Jun 4, 2009 at 4:38 AM, Myriam wrote:
>
> Hi,
>
> I have done (and seems OK, no error message) the low level analysis of
> the GenomeWideSNP_6.0 for preparing the analysis of my Affymetrix
> results in 50 samples.
> However, I cannot get through the steps of defining the CEL files set.
> I have put all the CEL files in rawData/CLP/GenomeWideSNP_6.0 folder.
> How should I define the set of CEL files to be analysed and which are
> contained in that subfolder?
> Tried command:
> cs <- AffymetrixCelSet$byName("CLP", cdf=cdf)
> but error: AffymetrixCelSet not found
The name of the folder containing the CEL files should match the name
of the chip type exactly. In your case it should be
rawData/CLP/GenomeWideSNP_6.0
not
rawData/CLP/GenomeWideSNP_6
Does this work now ?
For future posts: it's better to give the complete R output; In your
case aroma.affymetrix probably reports something like:
Cannot create AffymetrixCelSet. *No such directory: CLP/GenomeWideSNP_6*
which tells you (and us) where the problem comes from.
Best,
Pierre
>
> I am a bit lost, as a beginner. Sorry to bother but hopefully one of
> you can help me?
>
> Thanks in advance,
> Myriam
>
> >
>
--~--~-~--~~~---~--~~
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.
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For more options, visit this group at
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-~--~~~~--~~--~--~---
[aroma.affymetrix] Re: After low level analysis.
Hi David,
First, a remark: it seems you're using CRMA v1; I recommend that you
use CRMA v2 instead, see this vignette:
http://groups.google.com/group/aroma-affymetrix/web/estimation-of-total-copy-numbers-using-the-crma-v2-method
At the end of this vignette there is a paragraph explaining how to
plot total copy numbers along a chromosome. You can do the same with
your current 'cesN', i.e. :
## define units of interest
units <- getUnitsOnChromosome(gi, chromosome=2, region=c(81,86)*1e6)
pos <- getPositions(gi, units=units)
## get the estimates for the first array
ce <- getFile(cesN, 1)
theta <- extractTheta(ce, units=units)
'pos' contains the position of the SNP, and 'theta' the normalized
(total) intensities. Alternatively you can also do
df <- extractChromosomalDataFrame(ce, units=units)
which with the data of the above vignette will look like:
> str(df)
> 'data.frame': 2901 obs. of 6 variables:
$ unit: int 1035784 1035785 776062 742910 1035786
1035783 1035788 419702 1035789 1035790 ...
$ group : int 1 1 1 1 1 1 1 1 1 1 ...
$ cell: int 1976248 1976249 1551502 1485198 1976250
1976247 1976252 838782 1976253 1976254 ...
$ chromosome : int 2 2 2 2 2 2 2 2 2 2 ...
$ physicalPosition: int 81001208 81001975 81005617 81006134 81009408
81009733 81016544 81016718 81017018 81023108 ...
$ NA06985 : num 1817 778 2586 3323 1080 ...
You can also do this for all arrays at once:
df <- extractChromosomalDataFrame(cesN, units=units)
Cheers,
Pierre.
On Thu, May 14, 2009 at 10:59 AM, David wrote:
>
> Hi Henrik!
>
> I´m working with the following vignette ( for the Affymetrix 5.0):
>
> library(aroma.affymetrix)
> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_5", tags="Full,r2")
> print(cdf)
> gi <- getGenomeInformation(cdf)
> print(gi)
> cs <- AffymetrixCelSet$byName("tumoresAna", cdf=cdf)
> print(cs)
> acc <- AllelicCrosstalkCalibration(cs)
> print(acc)
> csC <- process(acc, verbose=verbose)
> print(csC)
> plm <- AvgCnPlm(csC, mergeStrands=TRUE, combineAlleles=TRUE, shift=
> +300)
> print(plm)
> fit(plm, verbose=verbose)
> ces <- getChipEffectSet(plm)
> print(ces)
> fln <- FragmentLengthNormalization(ces)
> print(fln)
> cesN <- process(fln, verbose=verbose)
> print(cesN)
>
> Everything runs!
>
> But from this point forward I would like to analyze data, SNP by SNP,
> so:
>
> I wonder how could I analyze the intensity value of each SNP?
> How could I read both values, the normalized intensity and the locus
> for each SNP?
> I would like to see all markers as a sequence.
>
> Thx in advance!
>
> David
> >
>
--~--~-~--~~~---~--~~
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[aroma.affymetrix] Re: A question about Total Copy Number Analysis (5.0 & 6.0)
Hi Jing, You have probably already figured this out by yourself already now, but extractDataFrame is what you are after. However it is meant to extract data from *subsets* of units, not for all units at the same time. Otherwise it is likely that you will run into memory problems. One thing you can do if you reall y need all this information in the same file is to use extractDataFrame on chunks of units and append each chunk to the file. Hope this helps, Pierre. On Fri, Apr 24, 2009 at 9:56 AM, jing ma wrote: > Dear Henrik, > > I'm analyzing some Affy SNP 6.0 array data and I followed the tutorial > "Total Copy Number Analysis (5.0 & 6.0)". I did all the steps from > "low-level analysis" till "PCR fragment length normalization" and stopped > at: > > fln <- FragmentLengthNormalization(ces) > cesN <- process(fln, verbose=verbose) > > Now, I want to output all the preprocessed and normalized signal estimates > for each marker (SNP and CN, totally 1881415 of them) in each sample in the > following format: > > MarkerID Chromosome Position sampleID-1 sampleID-2 ... sampleID-m > > > What functions should I use (extractMatrix or extractDataFrame or...) to > have all the above information? > > Thanks very much for your time! > > Jing > > Jing Ma > St. Jude Children's Research Hospital > > > > --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: little mistake at "estimation-of-total-copy-numbers-using-the-crma-v2-method" page?
Hi, Thanks, that's fixed now. Pierre. On Sat, Apr 25, 2009 at 4:56 AM, mako wrote: > > Hi, Henrik and members > > At first, congratulations on 3 years anniversary! > > I may find little mistake at following URL. > http://groups.google.com/group/aroma-affymetrix/web/estimation-of-total-copy-numbers-using-the-crma-v2-method > > start paste > Step 3 - Probe summarization > (snip..) > "Here we choose to fit allele-specific CN estimates", because we can > always get total CN signals downstreams. > plm <- AvgCnPlm(csN, mergeStrands=TRUE, combineAlleles=TRUE) > end paste > > I think "Here we choose to fit allele-specific CN estimates" is > incorrect. It seems that "Here we choose to fit total CN signals > estimate". > if so, I would be grateful if you could correct it. > > -- > Kohda Masakazu > > Research Center for Genomic Medicine > Saitama Medical University > > > --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: accessing CnChipEffectSet
Hi Michael, On Tue, May 5, 2009 at 2:01 PM, mbaudis wrote: > > Dear all, > > when plotting local copy number values after normalization/chip > effects etc., one has to load the CnChipEffectSet (e.g.: > > cdf <- getCdf(cesN) > gi <- getGenomeInformation(cdf) > > Is there a shortcut to load the cesN object, besides running an > analysis script? although this wouldn't take too long, if one has kept > the whole file structure after analysis, it is way too much for CGIs > etc. Is there a shortcut I am not aware of? > Try using CnChipEffectSet$byName. For example if you wish to work with the total copy number data generated here : http://groups.google.com/group/aroma-affymetrix/web/estimation-of-total-copy-numbers-using-the-crma-v2-method you can do: verbose <- Arguments$getVerbose(-8, timestamp=TRUE) chipType <- "GenomeWideSNP_6" dataset <- "HapMap270,6.0,CEU,testSet"; tags <- "ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY"; cesN <- CnChipEffectSet$byName(dataset, tags=tags, chipType=chipType, mergeStrands=TRUE, combineAlleles=TRUE, verbose=log); of course the tags and other options have to be adapted to the analysis you did in the first place. Hope this helps, Pierre. > 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: LOH / UPD analysis
Hi Michael, Sorry for the very late reply. As you probably know most methods infer regions of LOH using Hidden Markov Models on genotype calls. In terms of software, you are probably aware of dChipSNP, which is certainly a good candidate. I am not sure whether Birdsuite from the Broad explicitly infers LOH but it might. You might also want to consider the recent VanillaICE Bioconductor package, which has two interesting features: 1) if copy number estimates are available they can be incorporated to the inference (not sure if this is what you are after if there are only few CNAs in your data, but it could be worth testing) and 2) it is able to incorporate the confidence of genotype (and copy number) calls into the model, if available. http://bioconductor.org/packages/2.3/bioc/html/VanillaICE.html An helpful thing quoted from the vignette of the SNPchip package: "An example of using oligo to process a batch of 209 Affymetrix 100k CEL files and VanillaICE to identify regions of alterations are provided in the hapmap100k vignette in the directory inst/testing of the VanillaICE package." This means that you should be able to estimate these regions of LOH using oligo and VanillaICE. oligo uses the method CLRMM to call genotypes, and CRLMM does estimate confidences for genotype calls. In terms of preprocessing, oligo uses SNPRMA, an adaptation of RMA to SNP chips. We (Henrik, mostly) have been working on reproducing SNPRMA and CRLMM within aroma.affymetrix; we can do this for 500k arrays now. This means that we are close to being able to use other preprocessing methods than SNPRMA (e.g. CRMAv2) before CRLMM genotyping: the only missing piece is that CRLMM priors will have to be trained on data preprocessed by these alternative methods, and the function to estimate the priors is not available yet. For SNP 6.0 arrays we have been waiting for a new implementation of CRLMM to be released within oligo, I don't know whether this implementation is finalized now. Cheers, Pierre. On Wed, Feb 18, 2009 at 5:41 AM, mbaudis wrote: > > Hi Pierre, > > thanks for the offer. In the one project, we are looking into genetic > causes for Silver-Russel syndrome. So far, we have identified only few > recurring CNAs. However, one goal is to screen patients for UPDs (that > is, copy number neutral LOH), too; some regions (e.g. chromosome 7) > have been described previously in SRS. > > We have data from 250k SNP arrays and now from Affymetrix 6.0, too. We > usually screen patients only, with optional analysis of the parents in > case of "interesting" results. However, parent DNA may not be > available for all cases. > > For UPD analysis, we would be interested to have a package integrating > into the aroma.affymetrix data structure. Affy 6.0, and optional 250k > SNP would be the target arrays. Goal would be the detection of > abnormal LOH runs. > > I am aware of some software options for UPD analysis, but none of > those would plug in directly (at least to my knowledge). > > As said, any help is appreciated! > > Kind regards, > > Michael. > > > On Feb 17, 10:24 pm, Pierre Neuvial wrote: >> Hi Michael, >> >> I would be happy to try to help you here, but as Henrik suggested it's >> hard to answer without knowing what chip type you are using/planning >> to use... Can you be more specific ? >> >> Best, >> >> Pierre. > > > --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: to use an array list file
Hi, On Thu, Feb 12, 2009 at 4:25 PM, wukong wrote: > > I am wondering whether aroma-affymetrix can read in CEL files that are > scattered in several directories. > For example, the user may want to provide a text file specifying the > full paths of CEL files. > The reason is that I want to process these CEL files together, however > I don't want to copy them to one folder. Assuming that dataset1 and dataset2 are the names of two data sets you want to combine, that correspond to the same chip type, you can do cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full") csR1 <- AffymetrixCelSet$byName(dataset1, cdf=cdf) csR2 <- AffymetrixCelSet$byName(dataset2, cdf=cdf) csR <- append(csR1, csR2) Note that 'csR' will inherit the name of 'csR1'. To override this, do setFullName(csR, "Combined,tag1,tag2") print(csR) Then you can work with this combined csR as you would do for any data set. Note: Depending on the type of analysis you want to do, processing all CEL files together or individually, or by batches can lead to the same exact results: that's the power of single array methods (now it sounds like it's Henrik speaking...). This is the case for the CRMAv2 method for analyzing GenomeWide SNP chips. Thus, if a single array method is available to analyse your chip type, you might want to analyze the CEL files in each directory separately, and then combine the resulting 'ChipEffectSet', again using the 'append' method. This is discussed in the following thread: http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/b7d025724ff2deb5 This can be really useful if you want to analyze large number of chips. Hope this helps, Pierre. > > 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: LOH / UPD analysis
Hi Michael, I would be happy to try to help you here, but as Henrik suggested it's hard to answer without knowing what chip type you are using/planning to use... Can you be more specific ? Best, Pierre. On Tue, Feb 3, 2009 at 1:38 PM, Henrik Bengtsson wrote: > > Hi, > > there are no methods of such analysis available in aroma.affymetrix, > and there is no time line for implementing that. It is of course on > our wishlist, though. Note also that "LOH analysis" is rather > unspecific; there are many different ways to infer LOH, of which some > depend on what kind of data you have. > > I let other suggest alternative workflows. > > /Henrik > > On Tue, Feb 3, 2009 at 7:55 AM, mbaudis wrote: >> >> Dear all, >> >> AFAIK there is no method for LOH / UPD analysis implemented in a.a >> (yet?)? Is there a timeline for that? Does anybody have an established >> workflow for that, e.g. low level processing in a.a, and then using a >> separate solution? >> >> Any comments are appreciated! >> >> Thanks, >> >> Michael. >> >> IMB, University of Zurich >> www.progenetix.net >> > >> > > > > --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: Crash in using RmaCnPlm with combineAlleles = FALSE
Hi,
I don't know what the problem is. I tried your recipe on the HapMap
250K_Nsp and everything went fine:
library("aroma.affymetrix")
log <- Arguments$getVerbose(-8, timestamp=TRUE)
cdf <- AffymetrixCdfFile$byChipType("Mapping250K_Nsp")
cs <- AffymetrixCelSet$byName("HapMap270,500K,CEU,testSet", cdf=cdf)
Does this work for you on this HapMap data, or any other 250K_Nsp data set ?
Cheers,
Pierre.
On Thu, Jan 22, 2009 at 8:17 PM, Mike B wrote:
>
>
> I have tried out the new CRMAv2 method as described in the vignette
> "Estimation of total copy numbers using the CRMA v2 method", with the
> option of not combining A and B alleles, and for 250K chip type,
> "Mapping250K_Nsp". In doing this I have had the program crashing at
> what seems to be a bug in the underlying aroma.affymetrix code.
>
> My recipe is:
>
> # PROCESSING FOR "CRMAv2" METHOD
> # Input: 'cs' = CEL set of chip type "Mapping250K_Nsp"
>
> # (1) Allelic Crosstalk Calibration
> acc <- AllelicCrosstalkCalibration(cs, model="CRMAv2")
> csC <- process(acc, verbose=verbose)
>
> # (2) Base Position Normalization
> bpn <- BasePositionNormalization(csC, target="zero")
> csN <- process(bpn, verbose=verbose)
>
> # (3) Aggregate via RMA -- *not* combining alleles ...
> plm <- RmaCnPlm(csN, combineAlleles=FALSE, mergeStrands=TRUE)
> if (length(findUnitsTodo(plm, verbose=verbose)) > 0)
> fit(plm, verbose=verbose)
> ces <- getChipEffectSet(plm, verbose=verbose)
>
> # (4) Fragment Length Normalization
> fln <- FragmentLengthNormalization(ces, target="zero")
> cesN <- process(fln, verbose=verbose)
> theta <- extractTheta(cesN, verbose=verbose)
>
>
> In doing this I get the following error ...
>
>
> Error in updateCel(filename, indices = indices, intensities = values
> $intensities, :
> Number of 'intensities' values does not match the number of cell
> indices: 33308 != 66616
>
>
> The frame stack looks like ...
>
>
> Available environments had calls:
> 1: source("createAscnForChromosome.CRMAv2.source.R", echo = TRUE)
> 2: eval.with.vis(ei, envir)
> 3: eval.with.vis(expr, envir, enclos)
> 4: fit(plm, verbose = verbose)
> 5: fit.ProbeLevelModel(plm, verbose = verbose)
> 6: updateUnits(ces, units = units[uu], data = fit, verbose = less
> (verbose))
> 7: updateUnits.ChipEffectSet(ces, units = units[uu], data = fit,
> verbose = les
> 8: updateUnits(ce, cdf = cdf, data = dataOne, verbose = verbose)
> 9: updateUnits.ChipEffectFile(ce, cdf = cdf, data = dataOne, verbose =
> verbose
> 10: NextMethod("updateUnits", this, cdf = cdf, data = data, ...)
> 11: updateUnits.ParameterCelFile(ce, cdf = cdf, data = dataOne,
> verbose = verbo
> 12: NextMethod("updateUnits", this, cdf = cdf, data = data, ...,
> verbose = less
> 13: updateUnits.AffymetrixCelFile(ce, cdf = cdf, data = dataOne,
> verbose = verb
> 14: updateCelUnits(this$.pathname, data = data, ...)
> 15: updateCel(filename, indices = indices, intensities = values
> $intensities, st
> 16: stop("Number of 'intensities' values does not match the number of
> cell indi
>
>
>
>
>
> The problem is in part (3) where the RMA summarisation is done. The
> model fitting itself seems to be OK, or at least there is no crash
> there, but when the code tries to write the results to output files
> the crash occurs.
>
> What should be happening is that there should be 2 values per unit in
> the current chunk, and two indices per unit, saying where they should
> be written. Somehow this is not working, and the two numbers differ
> by a factor of two (33308 = 66616/2).
>
> I appreciate any help anyone can give me.
>
> Mike
>
>
> >
>
--~--~-~--~~~---~--~~
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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[aroma.affymetrix] Re: use a few normal samples as the reference set
Hi, I guess that if cesN is your chip-effect set (containing all 8 arrays), and if 1:4 are the normal samples you want to do cesNN <- extract(cesN, 1:4) ceR <- getAverageFile(cesNN, verbose=verbose) and then use this reference as you did before. Does this help ? Cheers, Pierre. On Tue, Jan 27, 2009 at 8:14 AM, Qicheng Ma wrote: > Hi Henrik, > > "For each location, the raw CN is calculated as the chip effect > relative to the chip effect of a normal reference sample. If no reference > sample is available, a robust average across all samples can be used > instead." > >Current documentation shows how to use the whole dataset (including > the test sample) as the reference sample. Could you please tell me how to > use a small number of normal samples as the reference sample, instead of the > all the samples, which include the test sample, as the reference sample, > e.g., we have 8 tumor samples, 4 normal samples, how to use the 4 normal > samples as the reference sample. > > Thanks, > > Qicheng > > > > --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: Experimental Design
Hi,
Your code looks OK, and 27 samples should be enough for the robust
average to be a reliable estimate "reference sample".
I guess that these experiments controls, is that right ? Can you share
an example of output of GLAD (by ChromosomeExplorer) and maybe CNAT on
a chromosome where it detects a copy number aberration, so that we can
guess where the problem comes from ?
Cheers,
Pierre.
PS: Would you mind sharing your name and affiliation ? I would be glad
(...) to know who I am writing to.
On Thu, Jan 22, 2009 at 1:51 PM, s...@rcega wrote:
>
> Hi, I´m working with the following vignette (with the 100k platform):
>
>
> library(aroma.affymetrix)
> #SetUp
> verbose <- Arguments$getVerbose(-8)
> timestampOn(verbose)
> name <- "controles"
> chipTypes <- c("Mapping50K_Hind240", "Mapping50K_Xba240")
> cdfs <- lapply(chipTypes, FUN=function(chipType) {
> AffymetrixCdfFile$byChipType(chipType)
> })
> print(cdfs)
> gis <- lapply(cdfs, getGenomeInformation)
> print(gis)
> sis <- lapply(cdfs, getSnpInformation)
> print(sis)
>
>
> cesNList <- list()
>
>
> chipType <- chipTypes[1]
> cs <- AffymetrixCelSet$byName(name, chipType=chipType)
> cs <- extract(cs, !isDuplicated(cs))
> print(cs)
> qn <- QuantileNormalization(cs)
> print(qn)
>
> csN <- process(qn, verbose=-20)
>
> plm <- RmaCnPlm(csN, combineAlleles=TRUE, mergeStrands=TRUE)
> print(plm)
> fit(plm, verbose=-20)
>
> ces <- getChipEffectSet(plm)
> fln <- FragmentLengthNormalization(ces)
> print(fln)
>
> cesNList[[chipType]] <- process(fln, verbose=verbose)
>
> chipType <- chipTypes[2]
> cs <- AffymetrixCelSet$byName(name, chipType=chipType)
> cs <- extract(cs, !isDuplicated(cs))
> print(cs)
> qn <- QuantileNormalization(cs)
> print(qn)
> csN <- process(qn, verbose=-20)
> plm <- RmaCnPlm(csN, combineAlleles=TRUE, mergeStrands=TRUE)
> print(plm)
> fit(plm, verbose=-20)
> ces <- getChipEffectSet(plm)
> fln <- FragmentLengthNormalization(ces)
> print(fln)
> cesNList[[chipType]] <- process(fln, verbose=verbose)
>
> glad <- GladModel(cesNList)
> print(glad)
> ce <- ChromosomeExplorer(glad)
> setArrays(ce, c("R007", "R014", "R015", "R035", "R039", "R052",
> "R062", "R064", "R072", "R075", "R081", "R102", "R106", "R108",
> "R111", "R115", "R121", "R124", "R183", "R189", "R208", "R221",
> "R230", "R240", "R247", "R208"))
> setAlias(ce, "Oscar_controls_2009")
> print(ce)
> process(ce, chromosomes=c
> (1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23),verbose=verbose)
>
> My experiment was designed for 27 tumors. It runs without errors but I
> ´m obtaining chromosomes complete gain or lost
>
> I wonder if I´m doing it right or I´m missing something or the number
> of experiments is not enough to find something significant. I´m
> comparing my results against a CNAT results and the number of segments
> are too much diferent.
>
> Thx 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.
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-~--~~~~--~~--~--~---
[aroma.affymetrix] Re: Wrong layout in plotAllelePairs
Hi again, Henrik pointed to me that plotAllelePairs.AllelicCrosstalkCalibration has an argument 'pairs' which can be used to specify the indexes of the pairs that one wants to plot. In my case plotAllelePairs(acc, array=array, pairs=1:6, what="input", xlim=xlim/3) does the job. Cheers, Pierre On Wed, Jan 14, 2009 at 11:56 AM, Pierre Neuvial wrote: > Hi, > > I have followed the steps of the CRMAv2 vignette: > > http://groups.google.com/group/aroma-affymetrix/web/estimation-of-total-copy-numbers-using-the-crma-v2-method > > using aroma.affymetrix version 1.0.0 and I got the following warning: > >> plotAllelePairs(acc, array=array, what="input", xlim=xlim/3) > Warning message: > In matrix(seq(length = nbrOfPairs), nrow = floor(sqrt(nbrOfPairs))) : > data length [7] is not a sub-multiple or multiple of the number of rows [2] > > This is because there are now *7* allele probe pair groups, not 6: > >> names(getSetsOfProbes(acc)$snp) > [1] "A/C" "A/G" "A/T" "C/G" "C/T" "G/T" "missing" > > As a result the plot layout is wrong: > >> nbrOfPairs <- length(getSetsOfProbes(acc)$snp) >> matrix(seq(length = nbrOfPairs), nrow = floor(sqrt(nbrOfPairs))) > [,1] [,2] [,3] [,4] > [1,]1357 > [2,]2461 > Warning message: > In matrix(seq(length = nbrOfPairs), nrow = floor(sqrt(nbrOfPairs))) : > data length [7] is not a sub-multiple or multiple of the number of rows [2] > > Maybe the easiest fix is to plot only the non "missing" allele pairs. > > Note that if one wants to use several central nucleotides instead of one, as > in > > alpha <- c(0.1, 0.075, 0.05, 0.03, 0.01, 0.0025, 1e-3, 1e-4); > acc <- AllelicCrosstalkCalibration(csR, alpha=alpha, pairBy="sequence", B=3) > > the number of allele pairs grows quickly: in this particular case > there are 96 allele pairs + 1 missing. > So maybe we it would make sense to hardcode a not to complex layout, > e. g. layout(matrix(seq(length=6, nrow=2))) ? > > Cheers, > > Pierre > >> sessionInfo() > R version 2.8.1 (2008-12-22) > i386-apple-darwin8.11.1 > > locale: > C > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] sfit_0.1.5 aroma.affymetrix_1.0.0 aroma.apd_0.1.3 > [4] R.huge_0.1.6 affxparser_1.14.0 aroma.core_1.0.0 > [7] aroma.light_1.9.2 digest_0.3.1 matrixStats_0.1.3 > [10] R.rsp_0.3.4R.cache_0.1.7 R.utils_1.1.3 > [13] R.oo_1.4.6 R.methodsS3_1.0.3 > --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Wrong layout in plotAllelePairs
Hi, I have followed the steps of the CRMAv2 vignette: http://groups.google.com/group/aroma-affymetrix/web/estimation-of-total-copy-numbers-using-the-crma-v2-method using aroma.affymetrix version 1.0.0 and I got the following warning: > plotAllelePairs(acc, array=array, what="input", xlim=xlim/3) Warning message: In matrix(seq(length = nbrOfPairs), nrow = floor(sqrt(nbrOfPairs))) : data length [7] is not a sub-multiple or multiple of the number of rows [2] This is because there are now *7* allele probe pair groups, not 6: > names(getSetsOfProbes(acc)$snp) [1] "A/C" "A/G" "A/T" "C/G" "C/T" "G/T" "missing" As a result the plot layout is wrong: > nbrOfPairs <- length(getSetsOfProbes(acc)$snp) > matrix(seq(length = nbrOfPairs), nrow = floor(sqrt(nbrOfPairs))) [,1] [,2] [,3] [,4] [1,]1357 [2,]2461 Warning message: In matrix(seq(length = nbrOfPairs), nrow = floor(sqrt(nbrOfPairs))) : data length [7] is not a sub-multiple or multiple of the number of rows [2] Maybe the easiest fix is to plot only the non "missing" allele pairs. Note that if one wants to use several central nucleotides instead of one, as in alpha <- c(0.1, 0.075, 0.05, 0.03, 0.01, 0.0025, 1e-3, 1e-4); acc <- AllelicCrosstalkCalibration(csR, alpha=alpha, pairBy="sequence", B=3) the number of allele pairs grows quickly: in this particular case there are 96 allele pairs + 1 missing. So maybe we it would make sense to hardcode a not to complex layout, e. g. layout(matrix(seq(length=6, nrow=2))) ? Cheers, Pierre > sessionInfo() R version 2.8.1 (2008-12-22) i386-apple-darwin8.11.1 locale: C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] sfit_0.1.5 aroma.affymetrix_1.0.0 aroma.apd_0.1.3 [4] R.huge_0.1.6 affxparser_1.14.0 aroma.core_1.0.0 [7] aroma.light_1.9.2 digest_0.3.1 matrixStats_0.1.3 [10] R.rsp_0.3.4R.cache_0.1.7 R.utils_1.1.3 [13] R.oo_1.4.6 R.methodsS3_1.0.3 --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: AllelicCrosstalkCalibration(..., model=CRMAv2, B=3)
Thanks Henrik, it worked.
Pierre
On Fri, Jan 9, 2009 at 10:14 PM, Henrik Bengtsson
wrote:
>
> Hi.
>
> On Fri, Jan 9, 2009 at 6:22 PM, Pierre Neuvial
> wrote:
>>
>> Hi,
>>
>> I would like to perform allelic crosstalk calibration using the 3
>> central nucleotides instead of 1, which is the default in CRMAv2. I've
>> tried this:
>>
>>> acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2", B=3, tags="B=3")
>
> The setup is (currently) that if you specify model="CRMAv2", this will
> override all other parameters. Instead you want to keep the default
> of 'model' (="asis") by leaving it out. To get the default CRMAv2
> parameters, but B=3, do:
>
> alpha <- c(0.1, 0.075, 0.05, 0.03, 0.01, 0.0025, 1e-3, 1e-4);
> acc <- AllelicCrosstalkCalibration(csR, alpha=alpha, pairBy="sequence", B=3)
>
> Note that when B != 1, you will automatically get an extra B=
> tag, e.g. "B=3".
>
> FYI, to *add* an extra tag, you must not forget to keep the other,
> which you specify by an asterisk, e.g. tags="*,myTag" or alternatively
> tags=c("*", "myTag").
>
> I'll see if I can find a way to interpret arguments model="CRMAv2",
> B=3, to mean CRMAv2 parameters but with B=3.
>
> Hope this works
>
> Henrik
>
>>
>> but parameter B is still 1:
>>
>>> print(acc)
>> AllelicCrosstalkCalibration:
>> Data set: HapMap270
>> Input tags: 6.0,CEU,testSet
>> User tags: B=3
>> Asterisk ('*') tags: ACC,ra,-XY
>> Output tags: 6.0,CEU,testSet,B=3
>> Number of files: 6 (395.13MB)
>> Platform: Affymetrix
>> Chip type: GenomeWideSNP_6,Full
>> Algorithm parameters: (rescaleBy: chr "all", targetAvg: num 2200,
>> subsetToAvg: chr "-XY", 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/HapMap270,6.0,CEU,testSet,B=3/GenomeWideSNP_6
>> Is done: FALSE
>> RAM: 0.00MB
>>
>> I guess that model="CRMAv2" forces B to be 1. Then how can I set up
>> another model with B=3 ?
>>
>> Thanks,
>>
>> Pierre
>>
>>
>>> library("aroma.affymetrix")
>> Loading required package: R.utils
>> Loading required package: R.oo
>> Loading required package: R.methodsS3
>> R.methodsS3 v1.0.3 (2008-07-02) successfully loaded. See ?R.methodsS3 for
>> help.
>> R.oo v1.4.6 (2008-08-11) successfully loaded. See ?R.oo for help.
>> R.utils v1.1.1 (2008-12-03) successfully loaded. See ?R.utils for help.
>> Loading required package: aroma.core
>> Loading required package: R.cache
>> R.cache v0.1.7 (2008-02-27) successfully loaded. See ?R.cache for help.
>> Loading required package: R.rsp
>> R.rsp v0.3.4 (2008-03-06) successfully loaded. See ?R.rsp for help.
>> Type browseRsp() to open the RSP main menu in your browser.
>> Loading required package: matrixStats
>> Loading required package: digest
>> Loading required package: aroma.light
>> aroma.light v1.9.2 (2008-09-10) successfully loaded. See ?aroma.light for
>> help.
>> aroma.core v0.9.6 (2008-12-04) successfully loaded. See ?aroma.core for help.
>> Loading required package: affxparser
>> Loading required package: R.huge
>> R.huge v0.1.6 (2008-07-03) successfully loaded. See ?R.huge for help.
>> Loading required package: aroma.apd
>> aroma.apd v0.1.3 (2006-06-14) successfully loaded. See ?aroma.apd for help.
>> aroma.affymetrix v0.9.6.4 (2008-12-17) successfully loaded. See
>> ?aroma.affymetrix for help.
>>> log <- verbose <- Arguments$getVerbose(-10, timestamp=TRUE)
>>> options(digits=4)
>>> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
>>> csR <- AffymetrixCelSet$byName("HapMap270,6.0,CEU,testSet", cdf=cdf)
>>> print(csR)
>> AffymetrixCelSet:
>> Name: HapMap270
>> Tags: 6.0,CEU,testSet
>> Path: rawData/HapMap270,6.0,CEU,testSet/GenomeWideSNP_6
>> Platform: Affymetrix
>> Chip type: GenomeWideSNP_6,Full
>> Number of arrays: 6
>> Names: NA06985, NA06991, ..., NA07019
>> Time period: 2007-03-06 12:13:04 -- 2007-03-06 19:17:16
>> Total file size: 395.13MB
>> RAM: 0.01MB
>> Warning messages:
>> 1: In rawToChar(raw) :
>> truncating string with embedded nul:
>> 'GenomeWideSNP_6\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0
[aroma.affymetrix] AllelicCrosstalkCalibration(..., model=CRMAv2, B=3)
Hi,
I would like to perform allelic crosstalk calibration using the 3
central nucleotides instead of 1, which is the default in CRMAv2. I've
tried this:
> acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2", B=3, tags="B=3")
but parameter B is still 1:
> print(acc)
AllelicCrosstalkCalibration:
Data set: HapMap270
Input tags: 6.0,CEU,testSet
User tags: B=3
Asterisk ('*') tags: ACC,ra,-XY
Output tags: 6.0,CEU,testSet,B=3
Number of files: 6 (395.13MB)
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full
Algorithm parameters: (rescaleBy: chr "all", targetAvg: num 2200,
subsetToAvg: chr "-XY", mergeShifts: logi TRUE, B: int 1, flavor: chr
"sfit", algorithmParameters:List of 3, ..$ 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/HapMap270,6.0,CEU,testSet,B=3/GenomeWideSNP_6
Is done: FALSE
RAM: 0.00MB
I guess that model="CRMAv2" forces B to be 1. Then how can I set up
another model with B=3 ?
Thanks,
Pierre
> library("aroma.affymetrix")
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.0.3 (2008-07-02) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.4.6 (2008-08-11) successfully loaded. See ?R.oo for help.
R.utils v1.1.1 (2008-12-03) successfully loaded. See ?R.utils for help.
Loading required package: aroma.core
Loading required package: R.cache
R.cache v0.1.7 (2008-02-27) successfully loaded. See ?R.cache for help.
Loading required package: R.rsp
R.rsp v0.3.4 (2008-03-06) successfully loaded. See ?R.rsp for help.
Type browseRsp() to open the RSP main menu in your browser.
Loading required package: matrixStats
Loading required package: digest
Loading required package: aroma.light
aroma.light v1.9.2 (2008-09-10) successfully loaded. See ?aroma.light for help.
aroma.core v0.9.6 (2008-12-04) successfully loaded. See ?aroma.core for help.
Loading required package: affxparser
Loading required package: R.huge
R.huge v0.1.6 (2008-07-03) successfully loaded. See ?R.huge for help.
Loading required package: aroma.apd
aroma.apd v0.1.3 (2006-06-14) successfully loaded. See ?aroma.apd for help.
aroma.affymetrix v0.9.6.4 (2008-12-17) successfully loaded. See
?aroma.affymetrix for help.
> log <- verbose <- Arguments$getVerbose(-10, timestamp=TRUE)
> options(digits=4)
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
> csR <- AffymetrixCelSet$byName("HapMap270,6.0,CEU,testSet", cdf=cdf)
> print(csR)
AffymetrixCelSet:
Name: HapMap270
Tags: 6.0,CEU,testSet
Path: rawData/HapMap270,6.0,CEU,testSet/GenomeWideSNP_6
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full
Number of arrays: 6
Names: NA06985, NA06991, ..., NA07019
Time period: 2007-03-06 12:13:04 -- 2007-03-06 19:17:16
Total file size: 395.13MB
RAM: 0.01MB
Warning messages:
1: In rawToChar(raw) :
truncating string with embedded nul:
'GenomeWideSNP_6\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
2: In rawToChar(raw) :
truncating string with embedded nul:
'GenomeWideSNP_6\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
3: In rawToChar(raw) :
truncating string with embedded nul:
'GenomeWideSNP_6\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
4: In rawToChar(raw) :
truncating string with embedded nul:
'GenomeWideSNP_6\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
5: In rawToChar(raw) :
truncating string with embedded nul:
'GenomeWideSNP_6\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
6: In rawToChar(raw) :
truncating string with embedded nul:
'GenomeWideSNP_6\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2", B=3, tags="B=3")
> print(acc)
AllelicCrosstalkCalibration:
Data set: HapMap270
Input tags: 6.0,CEU,testSet
User tags: B=3
Asterisk ('*') tags: ACC,ra,-XY
Output tags: 6.0,CEU,testSet,B=3
Number of files: 6 (395.13MB)
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full
Algorithm parameters: (rescaleBy: chr "all", targetAvg: num 2200,
subsetToAvg: chr "-XY", 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/HapMap270,6.0,CEU,testSet,B=3/GenomeWideSNP_6
[aroma.affymetrix] Re: Error in fragment length normalization
Hello Mike, I'm not sure what your problem is but it would certainly be helpful if you could post a complete code example, the corresponding output, and your sessionInfo(). That said, there have been several posts on the list about related problems, see e.g this one: http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/ccb58ee61f3f3aa/b8b552a10135c2b3?lnk=gst&q=cannot+fit+enzyme+to+target+function#b8b552a10135c2b3 Have you checked them ? Do they help ? Pierre On Tue, Jan 6, 2009 at 8:18 PM, Mike B wrote: > > In calling process.FragmentLengthNormalization() I am getting the > exception ... > > "Exception: Cannot fit target function to enzyme, because there are no > (finite) data points that are unique to this enzyme: 1" > > I am using 90 samples in the 50K Xba240 chip. > > What is the problem? I have run this successfully on a different > experiment with 20 CEL files. Is there a workaround? > > Mike > > > > --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
