ll.equal(data1, data2))
As a I said above, I would be surprised if you don't get that 'data1'
and 'data2' are equal/identical.
/Henrik
>
> Yes, i will check the pscbs vignette.
>
> Best
>
> Juanjo
>
>
> El martes, 15 de abril de 2014 18:43:42 UTC+2, He
R.rsp_0.15.0
> [9] splines_3.0.1 tools_3.0.1
>
> Any comments are wellcome!
>
> Thanks a lot
>
> Best
>
> Juanjo
>
>
>
>
> El lunes, 14 de abril de 2014 23:51:20 UTC+2, Henrik Bengtsson escribió:
>>
>> Hi,
>>
>> agree, that certai
Hi,
agree, that certainly doesn't look correct - but there's probably a
simple explanation/fix. Before anything else, what version of PSCBS
are you running, i.e. what's your sessionInfo(). Also, exactly what
does you script look like, and if you have a problematic sample you
could share with me,
Hi,
this sounds interesting. Could you elaborate a bit more on what you
are trying to do/achieve? A background may also help understand and
help to help you.
Cheers,
Henrik
On Thu, Apr 3, 2014 at 1:07 PM, Dan Wlodarski wrote:
>
> To whom it may concern:
>
> I'm a PhD candidate in the Wright
Hi,
aroma.affymetrix v2.12.0 has been released and is available on CRAN
(where the package is hosted). Update by:
source("http://aroma-project.org/hbLite.R";)
hbInstall("aroma.affymetrix")
This update contains a few bug fixes (thanks for the reports), a few
speedups plus some small bells an
ference. Please
report back to share you experience - there are some other user
benchmarks related to this on
http://aroma-project.org/howtos/ImproveProcessingTime
/Henrik
>
> Best,
> Damian
>
>
> On Tuesday, March 4, 2014 8:32:17 PM UTC-5, Henrik Bengtsson wrote:
>>
>>
seem okay or would you recommend any changes?
>
> thanks,
> Andrew Smith
>
> On Friday, December 3, 2010 1:18:23 AM UTC-5, Henrik Bengtsson wrote:
>>
>> Hi.
>>
>> On Thu, Dec 2, 2010 at 10:24 AM, Kai wrote:
>> > Hi Henrik,
>> >
>> >
Did lowering "memory/ram" solve your problem?
Also, an updated version of affxparser that no longer should overflow
by the integer multiplication is available (on Bioconductor).
Cheers,
Henrik
On Thu, Feb 27, 2014 at 12:36 PM, Henrik Bengtsson
wrote:
> Congratulations Damian,
>
> > Error in plot.window(xlim = xlim, ylim = ylim, log = log, yaxs = pars
>> > > $yaxs) :
>> > > NAs not allowed in 'ylim'
>> > >> plotRle(qamTr)
>> > > Error in plot.window(xlim = xlim, ylim = ylim, log = log, yaxs = pars
>>
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] preprocessCore_1.23.0 aroma.light_1.31.8 matr
On Fri, Feb 21, 2014 at 3:43 AM, Hans-Ulrich
wrote:
> Hi,
>
> I went through the code today and removed two lines from the function
> segmentByGLAD() from the arome.core package (version 2.11.0):
> # Cleaning out unknown parameters
> # keep <- (names(params) %in% names(formals));
> # params <-
argetDistribution=target)
csNs <- process(qn, verbose=verbose)
Hope this helps
/Henrik
>
> Kind regards,
>
> Damian Plichta
>
> On Monday, February 17, 2014 4:03:54 PM UTC-5, Henrik Bengtsson wrote:
>>
>> Hi.
>>
>> On Sun, Feb 16, 2014 at 6:
Hi.
On Sun, Feb 16, 2014 at 6:53 PM, Damian Plichta
wrote:
> Hi,
>
> I'm processing around 5500 affymetrix exon arrays. The
> RmaBackgroundCorrection() is pretty slow, 1-2 minutes/array. I played with
> setOption(aromaSettings, "memory/ram", X) and increased X up to 100 but it
> didn't have any e
a.core 2.11.0 is working fine. Thnaks a Lot
>
>
>
> Regards,
>
> Bibhu
>
>
>
> On Mon, Feb 3, 2014 at 12:04 AM, Henrik Bengtsson
> wrote:
>>
>> Hi,
>>
>> thanks for reporting with more details. I see that both of you are
>> using a
Hi,
thanks for reporting with more details. I see that both of you are
using aroma.core 2.11.1, and it could be that that version is causing
the problem. Try to revert back to aroma.core 2.11.0 (available on
CRAN) as:
install.packages("aroma.core")
Then restart(!) R and retry. Please let me
Alright, so Elizabeth Purdom found the missing files and kindly sent
them to me. I've now uploaded them the http://aroma-project.org
server and updated the links on http://aroma-project.org/node/40
accordingly.
Hope this helps
Henrik
On Tue, Jan 21, 2014 at 3:35 PM, Henrik Bengtsson
Hi,
thanks for reporting on this.
On Mon, Jan 20, 2014 at 2:09 PM, Guilherme Rocha wrote:
> Dear all,
>
> Does anybody know of any good tools for constructing a cdf file from affy
> pgf and clf files?
>
> It appears that such tools exist: http://www.aroma-project.org/node/40
>
> The problem is
On Tue, Jan 21, 2014 at 1:01 PM, Pierre Neuvial
wrote:
> 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 probl
Hi,
I'm not sure which chip type you're working on, but if it is
GenomeWideSNP_6, I've just made the na33 (hg19, dbSNP 137) UGP and UFL
annotation data files available:
http://aroma-project.org/chipTypes/GenomeWideSNP_6
The script used to build these files are:
https://r-forge.r-project.org/scm
On Sat, Jan 11, 2014 at 4:59 AM, wrote:
> Hi Jerry,
>
> Have you been able to resolve this issue?
> I ran into the same problem while working with matlab:
What's this sudden interest from the Matlab side and which Matlab
toolbox is the source of all this?
>
> Warning: The ChipType (Mouse430_2) o
On Sat, Nov 2, 2013 at 10:48 AM, wrote:
> Hi Philip,
>
>
>
> Thank you for your reply. OK, understood. However, FYI, I have applied
> "affyrma" as well, and again I got following error. Also, I am using this
> binary CDF (HuGene-1_1-st-v1,byTranscript-fsetid,pd.hugene.1.1.st.v1) that
> its siz
On Mon, Jan 6, 2014 at 1:34 AM, Hans-Ulrich
wrote:
> Hi Hernik,
>
> Clearing the cache as you suggested did the trick:
>
>
>> clearCache(dirs="aroma.affymetrix", recursive=TRUE, prompt=FALSE)
>
> Calculation of the sets of pobes with common SNP nucleotide pairs took much
> more time after clearing
Hi,
I haven't seen this before, but it certainly looks like something went
wrong when aroma tried to infer the SNP nucleotide pairs for that chip
type. This can either be due to issues reading the CDF or the ACS
file. Before continuing, check one more time that your CDF and ACS
files have identi
Hi,
I cannot reproduce this. First, it is not clear from your message
whether it is only this data set that cause problems or all data sets
you're trying including the ones you're saying used to work.
Second, start by verifying that your all your files are the same as
mine. Compare your output
Hi.
On Thu, Dec 26, 2013 at 12:47 PM, Sam Danziger wrote:
> I'm using FIRMA algorithm, and I would like to use an existing FIRMA model
> (for instance one trained on 50 arrays) on new data (e.g. 2 new arrays).
>
> I am able to train a FIRMA model (and an RMA model) quite easily using the
> doFIRM
preciate it if you give some advice on how to reduce such
> hyper-segmentation using CRMAv2, if any, according to your experience.
>
> best,
>
> Kim
>
>
>
>
>
> On Tue, Dec 17, 2013 at 11:37 PM, Henrik Bengtsson
> wrote:
>>
>> Hi.
>>
>> 1.
Hi.
1. It is not clear to me if you're saying that you get different
results now using a newer version of aroma.affymetrix that you used
before and on the same exact same data set, or something else.
Nothing intentionally have changed in the CRMAv2 pipeline (and I
cannot recall any recent updates
Fs
>> ('betaN'), I suspect a mismatched pair. Next, look at tumor vs normal
>> BAFs, e.g.
>>
>> plot(betaN, betaT, xlim=c(0,1), ylim=c(0,1))
>>
>> What do you get? You should see most data points scattered along the
>> diagonal line, similar t
articularly in upper-left and the lower-right
corners, your tumor normal pair is not from the same patient.
/Henrik
> Emilie
>
>
>
> On Thursday, December 12, 2013 6:01:48 PM UTC-5, Henrik Bengtsson wrote:
>
>> The tumor DH panel makes me believe that either your tumo
t; maybe an error in my normalization/plotting? Not all samples are like this,
> but it almost seems like the order of the of the probes is scrambled?
>
>
> Emilie
>
>
> On Thursday, December 5, 2013 1:08:46 PM UTC-5, Henrik Bengtsson wrote:
>>
>> Pierre beat me
Pierre beat me to this one. Comments below...
On Thu, Dec 5, 2013 at 9:20 AM, Pierre Neuvial
wrote:
> 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
>
> Wha
Hi,
aroma.affymetrix v2.11.0 and friends has been released and is
available on CRAN (where the package is hosted). Update by:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
This release is mainly about internal cleanups and adjusting to recent
changes in R 3.0.
Hi.
On Mon, Oct 7, 2013 at 4:57 AM, wrote:
>
> Dear aroma members,
>
> I wish to get your kind opinion regarding an issue. After running CRMAv2 and
> performing segmentation (CBS), I would like to run GISTIC analysis. As I
> understand I can run GISTIC from the segmented output. However, readi
Hi.
On Fri, Oct 4, 2013 at 8:19 PM, Ann Loraine wrote:
> I am working with ATH1/GPL198 Affymetrix microarrays and would like to use
> aroma to process a large set of arrays.
>
> I'm following the vignette on this page:
>
> http://www.aroma-project.org/vignettes/GeneSTArrayAnalysis
>
> But am stuc
Have a look here: http://aroma-project.org/setup/
/Henrik
On Wed, Sep 18, 2013 at 8:54 AM, wrote:
> Hi, I am dealing with Affy exon array data using aroma.affymetrix and had
> some problems while loading CEL files, see the following code:
>
>
>> cdf <-
>> AffymetrixCdfFile$byChipType("HuEx-1_0-
Hi,
for troubleshooting purposes, what does the following output:
library("R.filesets");
path <- "rawData/snp6_testing/GenomeWideSNP_6";
stopifnot(isDirectory(path));
files <- list.files(path=path, full.names=TRUE, all.files=TRUE);
sizes <- file.info(files)$size;
names(sizes) <- basename(files);
Hi, thanks. Could you please give a more precise description what you
want to do, e.g. what other method and what to do after that?
/Henrik
On Fri, Aug 9, 2013 at 12:47 AM, Koray Doğan Kaya
wrote:
> Hi,
> I like Aroma Affy. However I want to use some external probe level
> normalization other t
Hi,
aroma.affymetrix v2.10.0 and friends has been released and is
available on CRAN (where the package is hosted). Update by:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
This release is mainly about bug fixes, internal cleanups and some
minor speedups.
Chee
CC Genome Browser are
(still) hard coded. Please see:
https://groups.google.com/d/msg/aroma-affymetrix/r8CtCvdGWnE/jzQFMifxt2MJ
for more informations/details.
/Henrik
>
> Thanks a lot for the help!
>
> Sean
>
>
>
>
>
>
>
> On Fri, Aug 2, 2013 at 11:03 AM
On Mon, Aug 5, 2013 at 6:38 PM, Keith Ching wrote:
> Thanks Henrik this is working for me. I wasn't able to get it to recognize
> the new file in annotationData/genomes/Human/
> but I was able to change the default file in the package.
Did you try to rename it 'Human,chromosomes.txt' without any
Hi Keith.
On Mon, Jul 29, 2013 at 5:47 PM, Keith Ching wrote:
> sorry if this has been fixed already..
>
> i'm looking at a gene on chr9 at 138MB. I have segments that go out to
> 140MB.
> But the ChromosomeExplorer plot is truncated at 134MB for a SNP6 chip.
Thanks for spotting this.
>
> Is t
;- CbsModel(dsT, ref=dfR, tags="HapMapRef")
/H
>
> Thanks,
>
> Sean
>
>
>
> On Thu, Aug 1, 2013 at 6:00 PM, Henrik Bengtsson
> wrote:
>>
>> On Mon, Jul 29, 2013 at 7:45 PM, ying chen wrote:
>> > Hi Henrik,
>> > Thanks a lot for the help!
ll sm <- CbsModel(dsTR) work?
Skip the exportTotalCnRatioSet() call, and instead use:
sm <- CbsModel(dsTR, ref=dfR, tags="HapMapRef");
The 'tags' is just to add an informative tag to the output data set.
/Henrik
> Thanks again for your help!
> Sean
>
>
&
Hi.
On Fri, Jul 26, 2013 at 8:02 AM, sean nj wrote:
> Hi guys,
>
> I have a question regarding how to calculate raw copy numbers using common
> reference instead of average of all samples of the study. Basically I want
> to use average of HapMap270 samples as reference for all further copy number
Hi,
thanks for making me aware of this. This problem is specific to Windows.
First, install.packages("sfit", repos="http://R-Forge.R-project.org";)
should have worked, but, for unknown reasons, R-forge is not building
binaries for this package. Second, I've rebuild the binaries myself,
so the f
Hi,
see http://aroma-project.org/howtos/ImproveProcessingTime
Most importantly, increasing the RAM option will make a big difference.
/Henrik
On Mon, Jul 15, 2013 at 11:05 PM, Ryan Chow wrote:
> Hello,
>
> I'm looking to process 4000 HG-U133_Plus_2 microarrays using aroma, as it is
> memory-bo
On Wed, Jun 12, 2013 at 9:56 PM, Wei Tang wrote:
> Hi Henrik,
>
> Would you tell me where I can find the information of human build for the
> arrays?
> it seems you used hg18? am I correct?
Which genome version you use depends on which annotationData/ files
you use. Here are the ones we've built
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> States.1252LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C LC_TIME=English_United
> States.1252
> attached base p
I thought I fixed this in aroma.core 2.9.2, but I guess it wasn't enough.
For now try to load the R.cache package on startup - that should work
around the problem. Let me know if it works.
Henrik
On Jun 20, 2013 5:46 PM, "rangerq" wrote:
> Hi,
>
> I got an error when I processed a Affy Human Ge
of the Paired PSCBS (PDF)
vignette that is part of the PSCBS package.
/Henrik
>
>
> Many thanks,
>
> Wei
>
>
> On Thu, Jun 6, 2013 at 5:38 PM, Henrik Bengtsson
> wrote:
>>
>> On Thu, Jun 6, 2013 at 1:43 PM, Wei Tang wrote:
>> > Everything goes very
rt that they have the same number of samples:
# [doCBS() will do this too]
stopifnot(length(dsTTuple) == length(dsNTuple));
# Matched tumor-normal segmentation (pay attention to the verbose at
the beginning)
doCBS(dsTTuple, ref=dsNTuple, verbose=-10);
Hope this helps
Henrik
>
> Many thanks,
>
tal" "E1520T_Nsp,total"
>> [4] "E1521T_Nsp,total" "E1532T_Nsp,total" "E1535T_Nsp,total"
>> [7] "E1542T_Nsp,total" "E1546T_Nsp,total" "E1558T_Nsp,total"
>> [10] "E1566T_Nsp,total" &quo
raphics grDevices utils datasets methods base
>
> other attached packages:
> [1] R.cache_0.6.5 aroma.cn_1.3.3 DNAcopy_1.34.0
> [4] aroma.affymetrix_2.9.4 affxparser_1.32.1 aroma.apd_0.2.3
> [7] R.huge_0.4.1 aroma.light_1.30.2 aroma.core_2
f you plan to infer parent-specific CNs. If you don't know
yet, use doASCRMAv2(). Everything should work the same with doCBS().
/Henrik
>
> Many thanks,
>
> Wei
>
>
> On Thursday, May 30, 2013 6:05:55 PM UTC-4, Henrik Bengtsson wrote:
>>
>> Hi,
>>
&g
ysis analysis
> because QuantileNormalization could affect the relationship between pairs of
> coexpressed genes.
>
> If not, could you suggest me another package I could use? Is limma my only
> option ?
> Looking forward hearing from you
> Best
>
> Jean-paul.
>
> Le jeudi 13 août
Hi,
I've done some updates to the help pages (e.g. ?doCBS), so before
anything I recommend to update to aroma.core 2.9.5 and
aroma.affymetrix 2.9.4:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
On Tue, May 28, 2013 at 9:37 AM, Wei Tang wrote:
> Hi aroma.affymetr
Hi.
On Wed, May 29, 2013 at 3:12 AM, shangzhong Li wrote:
> I am trying to analyse GSE 30321 datasets in R. However it has 295 samples
> in two files (one has 255 and another has 40). They have same platform.
> gset <- getGEO('GSE30321',GSEMatrix =TRUE)
> gives gset two elements. Does anyone kno
Hi Yadav,
thanks for reporting on this. It to me a while to reproduce it. A
quick fix would be to explicitly load the R.cache package, which is
the package that defines that missing getChecksum(). However, I've
fixed this in aroma.core v2.9.2, so you update the error should go
away. Update as
Hi all,
aroma.affymetrix v2.9.0 has been released and is available on CRAN
(where the package is hosted). Update by:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
This is mainly a maintenance update to meet some new CRAN
requirements. Interestingly, no bugs w
rguments$getReadablePath("AromaAnalysis/annotationData/HG-U133_Plus_2",
> mustExist = TRUE)
> - Arguments$getReadablePath() is local of the calling function
>
> Error: Pathname not found: AromaAnalysis/annotationData/HG-U133_Plus_2 (none
> of the parent dir
Hi.
On Tue, Apr 30, 2013 at 8:26 AM, nawin MOHAMMED wrote:
> hi Pierre,
>
> the anootationData is allocated by default in the aroma.affymetrix ?? is it
> ??? as its declare in the page of aroma :
>
> Aroma.affymetrix searches for CDF files in the annotationData/ directory of
> the current w
a$cell);
# Merge CDF annotation data with signals
data <- cbind(cdfData, Y);
# Save
# [see help("writeDataFrame.data.frame")]
pathname <- writeDataFrame(data, file="all_probes.txt",
header=list(chipType=getChipType(cdf)));
Again, not sure what you're go
Hi,
sorry for the long delay.
On Mon, Apr 1, 2013 at 7:21 AM, wrote:
> Dear forum,
>
> I am analyzing data of HuGene2.0-st arrays. I am using aroma for
> pre-processing and used limma for differential expression. However after
> multiple testing I lost significance so I want to perform variance
gt; Today's Topic Summary
>>Group:
>>http://groups.google.com/group/aroma-affymetrix/topics
>><http://groups.google.com/group/aroma-affymetrix/topics>
>>
>>* PSCBS and callNTCN() (Was: Re: [aroma.affymetrix] Digest for
>>aroma-affymetrix@googleg
d on bootstrapped segment TCN levels
fit <- callNTCN(fit, delta=deltaCN, verbose=-20);
printf("Number of NTCN segments: %d\n", sum(getSegments(fit)$ntcnCall,
na.rm=TRUE));
## Number of NTCN segments: 303
toPNG(sampleName, tags="tracks,avgDH=median,AB+LOH+NTCN", aspectRatio=
this. See a couple of remaining issues below.
> /Ingrid
>
>
>
> On Wednesday, 27 March 2013 18:16:07 UTC+11, Henrik Bengtsson wrote:
>>
>> On Tue, Mar 26, 2013 at 10:03 PM, Ingrid Lönnstedt
>> wrote:
>> >
>> > Thank you Henrik!
>> &
Hi Jonathan.
On Thu, Apr 11, 2013 at 6:38 AM, wrote:
> Hi all,
>
> I suppose this is a simple enough task even for a newbie like me, I have
> found a similar related post but I have two questions:
>
> My First Question when I use the following commands in R:
>
> library(aroma.affymetrix)
>
> cdf
ld me, but are you working
with fresh frozen tumors or FFPE ones? The latter are often messy and
I haven't seen any methods that rescue their signals very well.
/Henrik
> All the best,
> Ingrid
>
>
> On Saturday, 23 March 2013 05:03:50 UTC+11, Henrik Bengtsson wrote:
>>
M: 0.00 MB
> Chip type: GenomeWideSNP_6,Full
>
> Thanks in advance
> Uma
>
> On Sat, Mar 23, 2013 at 5:52 PM, Uma Shankavaram
> wrote:
>>
>> Sorry, I guess I overlooked it. Many thanks for the help.
>>
>> Uma
>>
>>
>> On Sat, Mar 23, 201
<- Arguments$getVerbose(-8, timestamp=TRUE)
I've changed 'log' to 'verbose', because that will always work.
/H
>
> Thx
>
> Uma
>
>
> On Sat, Mar 23, 2013 at 5:32 PM, Henrik Bengtsson
> wrote:
>>
>> On Sat, Mar 23, 2013 at 2:29 PM, Uma Sha
57941, GSM557942
> Color maps: sqrt,yellow
> Chip type: GenomeWideSNP_6.Full
> Samples: GSM557940, GSM557941, GSM557942
> Aliases: GSM557940, GSM557941, GSM557942
> [1] FALSE
>
>
> Uma
>
> On Sat, Mar 23, 2013 at 5:05 PM, Henrik Bengtsson
> wrote:
>>
>&g
ma.affymetrix], or (b) GenomeWideSNP_(5|6) [which is not ported].
In other words, it's the internal oligo:::genotypeOne() that needs to
be ported.
>
> Anyway, thank you to share with us the aroma.affymetrix suite.
You're welcome - hopefully it makes everyday science a bit easier.
/Henrik
&g
Install() to never install from R-forge. FYI, don't install
from R-forge, because that contains my non-official under-construction
and non-tested updates.
On Sat, Mar 23, 2013 at 12:24 PM, Henrik Bengtsson
wrote:
> I can reproduce this - very odd. I'll investigate a fix it. In the
>
I can reproduce this - very odd. I'll investigate a fix it. In the
meanwhile, install the aroma.* 2.8.0 versions via CRAN, e.g.
install.packages("aroma.core", repos="@CRAN@")
install.packages("aroma.affymetrix", repos="@CRAN@")
(Add repos="@CRAN@" to make sure not to install from other repositor
Hi Carles,
the quick answer it that aroma.affymetrix only implements the CRLMM
method for the 100K (Mapping50K_Xba142 and Mapping50K_Hind142) and
500K (Mapping250K_Nsp and Mapping250K_Sty) chip types. For newer
methods you need to turn to the Bioconductor 'oligo' package.
However, what are you
Hi Ingrid.
On Wed, Mar 20, 2013 at 4:45 PM, Ingrid Lönnstedt
wrote:
>
> Hi!
>
> I have segmented 56 SNP 6 tumour samples with segmentByNonPairedPSCBS(),
> and like to call allelic balance segments with callAB() as required, I
> understand, before I can call neutral TCNs with callNTCN().
First, I
unctional
> Genomics.
> University of Cambridge. Cancer Research UK Cambridge Institute.
> Li Ka Shing Centre, Robinson Way.
> Cambridge CB2 0RE
> England
>
> Please note that my email address will be changing to:
> oscar.ru...@cruk.cam.ac.uk
>
>
>
>>
>&
ellow, Caldas Lab, Breast Cancer Functional
> Genomics.
> University of Cambridge. Cancer Research UK Cambridge Institute.
> Li Ka Shing Centre, Robinson Way.
> Cambridge CB2 0RE
> England
>
> Please note that my email address will be changing to:
> oscar.ru...@cruk.cam.ac.uk
Hi "CK",
On Fri, Feb 1, 2013 at 6:56 AM, wrote:
> Hi,
>
>i am a new user of aroma.affymetrix , can I know how do one export
> intensity values from all the samples into matrix form? ( i have 57 CEL
> files), since i would like to use those to perform pca and check for batch
> effect.
If you
On Thu, Feb 7, 2013 at 5:33 PM, Henrik Bengtsson
wrote:
> Hi,
>
> sorry for the delay - I've been "off the grid" since two weeks.
>
> On Thu, Jan 24, 2013 at 4:09 AM, Oscar Rueda
> wrote:
>> Dear all,
>>
>> I'm trying to run PSCBS on 12
Hi,
sorry for the delay - I've been "off the grid" since two weeks.
On Thu, Jan 24, 2013 at 4:09 AM, Oscar Rueda wrote:
> Dear all,
>
> I'm trying to run PSCBS on 126 matched pairs, but only 60 of them have run
> without errors. The last error I got was when running callAB:
>
>> deltaAB <- estim
On Mon, Feb 4, 2013 at 4:14 PM, wrote:
> Hi All,
>
> I was following the online viginette
> http://www.aroma-project.org/howtos/exportTotalCnRatioSet to export total
> Copy Number Ratios, i have ran CRMAv2 without problem, but when I try to do
> the following i got the error in cdf, anyone ha
Just to close this (old) thread:
On Mon, May 7, 2012 at 1:07 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
Try with calmate v0.10.0, which you can install by:
source("http://aroma-project.org/hbLite.R";);
hbInstall("calmate")
Let me know if this solves it for you.
/Henrik
On Fri, Jan 4, 2013 at 3:32 PM, Siyuan Zheng wrote:
> Thank you.
>
>
> On Fri, Jan 4, 2
R.filesets_1.9.0
> [16] R.utils_1.19.3 R.oo_1.11.4R.methodsS3_1.4.2
>
> loaded via a namespace (and not attached):
> [1] digest_0.6.0 PSCBS_0.30.0
>
> Have you seen this before?
> Thanks.
>
> Siyuan
> MD Anderson
>
>
>
> On Friday, Janu
What's your session info after loading aroma.affymetrix and calmate?
Henrik
On Jan 4, 2013 9:59 PM, "Zheng Siyuan" wrote:
>
> Hi,
> I have been using Calmate to process my affy SNP6 array data. The goal is
to call calibrated allele specific copy number. However, I ran into an
error following the
Hi.
On Thu, Jan 3, 2013 at 12:11 AM, Saman Amini wrote:
>
> Hi all,
>
> I am using aroma.affymetrix to get the segmented paired copy numbers for raw
> CELL files and CDF annotation files. The path and the R script are shown
> below.
> As you can see in the result table, the last column is showi
Hi all,
aroma.affymetrix v2.8.0 has been released. Update by:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
Bug fixes, improved fault tolerance, more unique caching, improved
creation of CDF files from Bioconductor PDInfo packages and more. As
usual, details b
Hi.
On Mon, Dec 10, 2012 at 8:49 AM, Hooiveld, Guido wrote:
> Hi Henrik,
>
>
>
> I am testing the binary CDF files I created for various Gene ST arrays (re:
> discussion last Friday), but I run into problems.
>
> An error is occurring when reading the cell files. According to the change
> log thi
Hi.
On Fri, Dec 7, 2012 at 7:04 PM, zhouzaiwei wrote:
> Hi, everyone, I want to use FIRMAGene to analysis differencial splicing of
> hugene-1.0-st array ,there is no overlap between Ensembl identifiers from
> getUnitNames() and Affymetrix identifiers in 'hgnetaffx'.follows my code:
>>library(arom
On Fri, Dec 7, 2012 at 2:09 PM, Hooiveld, Guido wrote:
> Hi,
> Sorry for the indistinctness. You are correct; these are indeed R-packages
> (CDF environments), thus not *files*. However, it won't be much effort to
> also make them available as files. I/we will have a look at it the next
> coupl
such. (*) BTW, that script has
now been replaced by
http://aroma-project.org/howtos/createCdfFromBioconductorPlatformDesignInfo
Thanks,
Henrik
> HTH,
> Guido
>
> -Original Message-
> From: aroma-affymetrix@googlegroups.com
> [mailto:aroma-affymetrix@googlegroups.com] O
On Thu, Dec 6, 2012 at 5:54 AM, Maria Traka wrote:
> Hi guys,
> probably you've already given the answer somewhere but can i use
> aroma.affymetrix to analyse Affymetrix 2.0 ST arrays (human and mouse)?
> Presumably the same way as 1.0 arrays?
I'm not working with those myself, and I don't know t
Hi again.
On Fri, Nov 30, 2012 at 12:44 PM, Sam Danziger wrote:
> I've been trying to use FIRMA analysis
> (http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis) on my
> mouse arrays (
> Mouse Exon 1.0 ST Array -
> http://aroma-project.org/chipTypes/MoEx-1_0-st-v1).
>
> It looks li
On Fri, Nov 30, 2012 at 12:44 PM, Sam Danziger wrote:
> I've been trying to use FIRMA analysis
> (http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis) on my
> mouse arrays (
> Mouse Exon 1.0 ST Array -
> http://aroma-project.org/chipTypes/MoEx-1_0-st-v1).
>
> It looks like the scri
[I'm reply to each of your questions in three separate threads to make
it easier to follow]
Hi.
On Fri, Nov 30, 2012 at 12:44 PM, Sam Danziger wrote:
> I've been trying to use FIRMA analysis
> (http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis) on my
> mouse arrays (
> Mouse Ex
1.50
> Number of QC units: 4
>> stopifnot(identical(getChecksum(cdfM),
>> "3a797e24a62f4f2e5214a6bf819151da"));
>> getChecksum(cdfM)
> [1] "3a797e24a62f4f2e5214a6bf819151da"
>
> Ioana
>
> On Tuesday, 27 November 2012 21:40:54 UTC+2, Henrik Bengtsson wrote:
>>
ever, there was a bug in the version you
used causing only setRam() to work, which is why I told you to use
that one. If you install the latest version:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
you should also get aroma.core v
70 216.7 83594476 637.8 130588565 996.4
> Fitting 1 arrays...done
> Estimating single-probe CN units...done
>> str(units1);
> int [1:945826] 935590 935591 935592 935593 935594 935595 935596 935597
> 935598 935599 ...
>> units <- findUnitsTodo(plm);
>> str(units);
eed 1.1GB and with
RAM=1.0 it will use up to 1.7GB of RAM.
How much RAM/memory do you have on your computer?
/Henrik
>
>
>
>
>
>
> At 2012-11-27 13:57:24,"Henrik Bengtsson-4 [via aroma.affymetrix]" <[hidden
> email]> wrote:
>
> Hi,
>
> first thing
101 - 200 of 1062 matches
Mail list logo
