[BioC] Mouse Gene ST v1 CDF Issues (MoGene10stv1): Failure of affyPLM and pdfInfoBuilder
White, Peter
Peter.White at nationwidechildrens.org
Tue Dec 2 17:56:30 CET 2008
Dear Jim,
Thanks for responding so quickly - it worked! I installed RTools version
2.9, installed Inno Setup (not sure if it was needed but I didn't have
it), and updated Cygwin. Also I reordered the path so that RTools came
first, and added as missing path statement for mitext and html help as
outlined at
http://cran.r-project.org/doc/manuals/R-admin.html#The-Windows-toolset.
Not sure which of these steps was at fault but once that was done the
package compiled fine and I was able to process my Gene ST cel files
with Oligo.
If anyone has any further thoughts on affyPLM and the Gene ST arrays, or
the issues I highlighted with the Affy annotation files and inconsistent
probe information, I would appreciate it. Using pdInfoBuilder the
resulting mouse Gene ST annotation file has 35,557 ids (note this is 10
less than is found in the MoGene-1_0-st-v1.na26.mm9.transcript.csv file,
which has 35,567??). Using the unsupported CDF with either makecdfenv or
aroma.affymetrix gives 35,512. It's probably just control probesets that
are being lost, but I am a little concerned that none of these methods
returns the 35,605 distinct transcript IDs found in the
MoGene-1_0-st-v1.probe.tab file from Affy.
Thanks.
Peter
> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at med.umich.edu]
> Sent: Tuesday, December 02, 2008 9:32 AM
> To: White, Peter
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Mouse Gene ST v1 CDF Issues (MoGene10stv1):
Failure
> of affyPLM and pdfInfoBuilder
>
> Hi Peter,
>
> I won't comment on aroma.affymetrix, nor building cdf packages using
> makecdfenv as the former has its own mailing list and the latter isn't
> really supported - the list archive you quote is Ben Bolstad showing
> that you _could_ use makecdfenv, but then raising several questions
> that
> have not been resolved to my knowledge.
>
> As for building a pdInfoPackage, this works fine for me:
>
> > makePdInfoPackage(pkg, destDir=".")
> Creating package in ./pd.mogene.1.0.st.v1
> loadUnitsByBatch took 46.92 sec
> loadAffyCsv took 19.19 sec
> loadAffySeqCsv took 51.92 sec
> DB sort, index creation took 20.82 sec
> [1] TRUE
> Warning messages:
> 1: In is.na(x) : is.na() applied to non-(list or vector) of type
'NULL'
> 2: In is.na(x) : is.na() applied to non-(list or vector) of type
'NULL'
> > sessionInfo()
> R version 2.8.0 (2008-10-20)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] splines tools stats graphics grDevices datasets utils
> [8] methods base
>
> other attached packages:
> [1] pdInfoBuilder_1.6.0 oligo_1.6.0 oligoClasses_1.4.0
> [4] AnnotationDbi_1.4.0 preprocessCore_1.4.0 affxparser_1.14.0
> [7] RSQLite_0.7-1 DBI_0.2-4 Biobase_2.2.0
>
> Note that it would have been helpful for you to give us your
> sessionInfo() as well.
>
> The install went fine:
>
> ---------- Making package pd.mogene.1.0.st.v1 ------------
> adding build stamp to DESCRIPTION
> installing NAMESPACE file and metadata
> installing R files
> installing inst files
> preparing package pd.mogene.1.0.st.v1 for lazy loading
> Loading required package: RSQLite
> Loading required package: DBI
> Loading required package: oligoClasses
> Loading required package: Biobase
> Loading required package: tools
>
> Welcome to Bioconductor
>
> Vignettes contain introductory material. To view, type
> 'openVignette()'. To cite Bioconductor, see
> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> no man files in this package
> installing indices
> installing help
> adding MD5 sums
>
> * DONE (pd.mogene.1.0.st.v1)
>
> I would bet that your problem stems from having Cygwin installed as
> well
> as the Windows Toolset (Rtools). If you don't have your path set
> correctly, then you may find the wrong version of certain tools and
> things won't build correctly.
>
> I have personally found that Cygwin is problematic when installed, and
> can make matters worse if you then uninstall because for whatever
> reason
> you then cannot find certain tools. Does the install directory of the
> Windows Toolset reside higher up in the PATH than Cygwin?
>
> Best,
>
> Jim
>
>
>
> Peter White wrote:
> >> I am having some issues with the Affymetrix Mouse Gene ST 1.0 array
> > (MoGene10stv1) and bioconductor. I can see that there are issues
> regarding this
> > array and the unsupported CDF that can be downloaded from Affy but I
> was able
> > to create the mogene10stv1cdf library as outlined in the thread:
> >
> > https://stat.ethz.ch/pipermail/bioc-devel/2007-October/001403.html
> >
> > I have processed the data using both Bioconductors Affy Package and
> the
> > aroma.Affymetrix package but get different results. I believe the
> issue is that
> > aroma is using the affyPLM model. I wanted to check this using the
> bioconductor
> > affyPLM package but it will not work:
> >
> > Method 1 - works fine:
> >
> > library(affy)
> > AffyRaw <- ReadAffy()
> > AffyEset <- rma(AffyRaw)
> > data.affy <- exprs(AffyEset)
> >
> > Method 2 - fails:
> >
> > library(affyPLM)
> > AffyRaw <- ReadAffy()
> > fit <- fitPLM(AffyRaw, verbos=9)
> >
> > Background correcting PM
> > Normalizing PM
> > Fitting models
> > Error in fitPLM(AffyRaw, verbos = 9) :
> > Realloc could not re-allocate (size 1150530304) memory
> >
> > I also tried the following but it still could not run:
> >
> > fit <- fitPLM(AffyRaw, output.param=list(weights=FALSE,
> residuals=FALSE,
> > varcov="none", resid.SE=FALSE))
> >
> > Finally, I dropped the number of arrays from 16 to 6, then down to
2,
> but still
> > no luck.
> >
> > So from piecing together different threads I wondered if the issue
> lied with
> > the unsupported CDF. So I attempted to use the pdfInfoBuilder /
oligo
> pipeline
> > as outlined in this thread:
> >
> >
>
http://article.gmane.org/gmane.science.biology.informatics.conductor/18
> 963/matc
> > h=mogene
> >
> > Again, I ran into problems:
> >
> >> pgfFile <- "MoGene-1_0-st-v1.r3.pgf"
> >> clfFile <- "MoGene-1_0-st-v1.r3.clf"
> >> transFile <- "MoGene-1_0-st-v1.na26.mm9.transcript.txt"
> >> probeFile <- "MoGene-1_0-st-v1.probe.tab"
> >> pkg <- new("AffyGenePDInfoPkgSeed", author="Peter White",
> email="peter.white
> > at nationwidechildrens.org", version="0.1.3", genomebuild="UCSC mm9,
> July
> > 2007", biocViews="AnnotationData", pgfFile=pgfFile, clfFile=clfFile,
> transFile=
> > transFile, probeFile=probeFile)
> >> makePdInfoPackage(pkg, destDir=".")
> > Creating package in ./pd.mogene.1.0.st.v1
> > loadUnitsByBatch took 54.44 sec
> > loadAffyCsv took 53.58 sec
> > loadAffySeqCsv took 80.68 sec
> > DB sort, index creation took 90.24 sec
> > [1] TRUE
> > Warning messages:
> > 1: In is.na(x) : is.na() applied to non-(list or vector) of type
> 'NULL'
> > 2: In is.na(x) : is.na() applied to non-(list or vector) of type
> 'NULL'
> >
> > Close R and start the command prompt and navigate to the directory
> with the
> > package:
> >
> > R CMD INSTALL pd.mogene.1.0.st.v1\
> >
> > installing to 'c:/PROGRA~2/R/R-28~1.0/library'
> >
> > ---------- Making package pd.mogene.1.0.st.v1 ------------
> > adding build stamp to DESCRIPTION
> > installing NAMESPACE file and metadata
> > installing R files
> > installing inst files
> > FIND: Parameter format not correct
> > make[2]: *** [c:/PROGRA~2/R/R-
> 28~1.0/library/pd.mogene.1.0.st.v1/inst] Error 2
> > make[1]: *** [all] Error 2
> > make: *** [pkg-pd.mogene.1.0.st.v1] Error 2
> > *** Installation of pd.mogene.1.0.st.v1 failed ***
> >
> > Removing 'c:/PROGRA~2/R/R-28~1.0/library/pd.mogene.1.0.st.v1'
> >
> > So the installation fails and I cannot work out why (I have RTools
> and Cygwin
> > installed). I did notice some inconsistencies in the annotation
files
> for these
> > arrays that can be downloaded from the Affy site and wondered if
> these could be
> > the source of the problem:
> >
> > 1. From the file MoGene-1_0-st-v1.probe.tab there are 35,605
> distinct
> > Transcript IDs.
> > 2. From the file MoGene-1_0-st-v1.na26.mm9.transcript.csv there are
> 35,567
> > transcript IDs . 38 transcripts ids are missing from this file. What
> are they
> > and why were they not included (10412488, 10412495, 10412500,
> 10412503,
> > 10412520, 10417226, 10417239, 10417269, 10417286, 10441511,
10468907,
> 10490232,
> > 10501544, 10535342, 10536010, 10536044, 10536095, 10536114,
10536118,
> 10536163,
> > 10550163, 10550775, 10560746, 10577361, 10598118, 10598141,
10598159,
> 10598207,
> > 10598220, 10598603, 10599086, 10606573, 10608226, 10608440,
10608551,
> 10608554,
> > 10608603, 10608606)
> > 3. From the file MoGene-1_0-st-v1.r3.cdf there are 35,512
Transcript
> IDs.
> > So we are now missing an additional 93 probe sets (all of these can
> be found in
> > the transcript file: 10338002, 10338005, 10338006, 10338007,
> 10338008,
> > 10338009, 10338010, 10338011, 10338012, 10338013, 10338014,
10338015,
> 10338016,
> > 10338018, 10338019, 10338020, 10338021, 10338022, 10338023,
10338024,
> 10338027,
> > 10338028, 10338030, 10338031, 10338032, 10338033, 10338034,
10338038,
> 10338039,
> > 10338040, 10338043, 10338045, 10338046, 10338048, 10338049,
10338050,
> 10338051,
> > 10338052, 10338053, 10338054, 10338055, 10338057, 10338058,
10338061,
> 10338062,
> > 10349381, 10350469, 10354866, 10361826, 10362430, 10362438,
10362444,
> 10362452,
> > 10362872, 10369759, 10374030, 10391748, 10395778, 10411504,
10422960,
> 10436496,
> > 10436660, 10446349, 10453719, 10457089, 10458079, 10460144,
10461932,
> 10481652,
> > 10482786, 10487009, 10498317, 10501216, 10502040, 10502768,
10503414,
> 10513713,
> > 10521665, 10532622, 10535929, 10546555, 10552810, 10553535,
10560364,
> 10582560,
> > 10582566, 10582570, 10582576, 10585872, 10586931, 10592453,
10601614,
> > 10602194). Again, why were they not included?
> >
> > BTW: I am using R 2.8.0 and the latest release of Bioconductor (2.3)
> on a
> > Windows XP 64-bit machine.
> >
> > Any help out there would be greatly appreciated.
> >
> > Thanks,
> >
> > Peter
> >
> > Peter White, Ph.D.
> > Director, Biomedical Genomics Core
> > Research Assistant Professor of Pediatrics
> > The Research Institute at
> > Nationwide Children's Hospital and
> > The Ohio State University
> >
> > Mailing Address:
> >
> > The Research Institute at
> > Nationwide Children's Hospital
> > 700 Children's Drive, W510
> > Columbus, OH 43205
> >
> > Office: (614) 355-2671
> > Lab: (614) 355-5252
> > Fax: (614) 722-2818
> > Web: http://genomics.nchresearch.org/
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Hildebrandt Lab
> 8220D MSRB III
> 1150 W. Medical Center Drive
> Ann Arbor MI 48109-0646
> 734-936-8662
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