I was wondering if anyone could give me advice on using Bioconductor to analyze .CEL files with the Affymetrix Mouse Gene 1.0 ST platform. I am a beginner with both R and bioconductor, and am using R version 2.12.1 with Bioconductor 2.7. A summary of what I have tried so far is below. Does anyone have any suggestions? Many thanks, Emily 1. My first try was basically my normal process for other Affymetrix arrays, tuned to what I thought were the right libraries for the Mouse Gene 1.0 array: > sampleNames <- c("deleted to save space") > celFileNames <- c("deleted to save space") > library("affy", lib.loc="/usr/local/lib/R/site-library") > library("gcrma", lib.loc="/usr/local/lib/R/site-library") > library(mogene10stprobeset.db, lib.loc="/usr/local/lib/R/site- library") > library(mogene10stv1cdf, lib.loc=="/usr/local/lib/R/site-library") > library(mogene10stv1probe, lib.loc=="/usr/local/lib/R/site-library") > eset.gcrma = justGCRMA(filenames=celFileNames, sampleNames=sampleNames, celfile.path="") Loading required package: AnnotationDbi Loading required package: org.Mm.eg.db Attaching package: 'RSQLite' The following object(s) are masked from 'package:RMySQL': dbBuildTableDefinition, isIdCurrent, safe.write Computing affinitiesError: length(prlen) == 1 is not TRUE Execution halted 2. I then tried the same procedure again, substituting the mogene10sttranscriptcluster.db for the mogene10stprobeset.db. I got the same error at the same point "length(prlen) == 1 is not TRUE". 3. I googled for help, and found two e-mails that seemed connected to what I was doing: A. https://stat.ethz.ch/pipermail/bioconductor/2008-July/023668.html B. http://article.gmane.org/gmane.science.biology.informatics.co nductor/18963 Because of these, I tried to read the .CEL files in using oligo package, but that was also unsuccessful, because I couldn't build the AffyGenePDInfoPkgSeed necessary for it. R version 2.12.1 (2010-12-16) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit) > library("pdInfoBuilder",lib.loc="/usr/local/lib/R/site-library") > pgfFile <- "MoGene-1_0-st-v1.r4.pgf" > clfFile <- "MoGene-1_0-st-v1.r4.clf" > transFile <- "MoGene-1_0-st-v1.na31.mm8.transcript.csv" > probeFile <- "MoGene-1_0-st-v1.probe.tab" > pkg <- new("AffyGenePDInfoPkgSeed", author = "Emily Merrill", email = "deleted here", version = "0.0.1", genomebuild = "August 2010", biocViews = "AnnotationData", pgfFile = pgfFile, clfFile = clfFile, transFile = transFile, probeFile = probeFile) > makePdInfoPackage(pkg,"/var/www/rdata/") ====================================================================== Building annotation package for Affymetrix Gene ST Array PGF.........: MoGene-1_0-st-v1.r4.pgf CLF.........: MoGene-1_0-st-v1.r4.clf Probeset....: MoGene-1_0-st-v1.probe.tab Transcript..: MoGene-1_0-st-v1.na31.mm8.transcript.csv Core MPS....: coreMps ====================================================================== Parsing file: MoGene-1_0-st-v1.r4.pgf... OK Parsing file: MoGene-1_0-st-v1.r4.clf... OK Creating initial table for probes... OK Creating dictionaries... OK Parsing file: MoGene-1_0-st-v1.probe.tab... OK Error in `[.data.frame`(probesets, , cols) : undefined columns selected In addition: 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'

Thank you very much to both Christian and Vincent! In the vignettes, both XPS and Oligo use only RMA processing on the object created by reading in the .CEL files. Is it possible/correct to do GCRMA processing on an Affymetrix Gene 1.0 ST array? I tried using Oligo first and I was able to read in the .CEL files using pd.mogene.1.0.st.v1. But, I couldn't find a way to make the gcrma() function accept an Oglio-created object. I am worried about encountering a similar problem with XPS. -Emily R version 2.12.1 (2010-12-16) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit) > celFileNames <- c("deleted here for space") > affyExpressionFS <- read.celfiles(celFileNames) Loading required package: pd.mogene.1.0.st.v1 Loading required package: RSQLite Loading required package: DBI Platform design info loaded. Reading in : <deleted here="" for="" space=""> > genePS <- rma(affyExpressionFS, target="probeset") Background correcting Normalizing Calculating Expression > eset.gcrma = gcrma(affyExpressionFS) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "indexProbes", for signature "GeneFeatureSet", "character"

Dear Emily, Alternatively, you could use the package xps, although package oligo does work with these arrays. As far as I know there should be no need to use pdInfoBuilder for MoGene ST arrays. Best regards Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._ On 3/25/11 6:26 PM, M. Emily Merrill wrote: > I was wondering if anyone could give me advice on using Bioconductor > to analyze .CEL files with the Affymetrix Mouse Gene 1.0 ST platform. > > I am a beginner with both R and bioconductor, and am using R version > 2.12.1 with Bioconductor 2.7. > > A summary of what I have tried so far is below. Does anyone have any > suggestions? > > Many thanks, > Emily > > > 1. My first try was basically my normal process for other Affymetrix > arrays, tuned to what I thought were the right libraries for the Mouse > Gene 1.0 array: >> sampleNames<- c("deleted to save space") >> celFileNames<- c("deleted to save space") >> library("affy", lib.loc="/usr/local/lib/R/site-library") >> library("gcrma", lib.loc="/usr/local/lib/R/site-library") >> library(mogene10stprobeset.db, lib.loc="/usr/local/lib/R/site- library") >> library(mogene10stv1cdf, lib.loc=="/usr/local/lib/R/site-library") >> library(mogene10stv1probe, lib.loc=="/usr/local/lib/R/site- library") >> eset.gcrma = justGCRMA(filenames=celFileNames, sampleNames=sampleNames, celfile.path="") > Loading required package: AnnotationDbi > Loading required package: org.Mm.eg.db > Attaching package: 'RSQLite' > The following object(s) are masked from 'package:RMySQL': > dbBuildTableDefinition, isIdCurrent, safe.write > Computing affinitiesError: length(prlen) == 1 is not TRUE > Execution halted > > 2. I then tried the same procedure again, substituting the > mogene10sttranscriptcluster.db for the mogene10stprobeset.db. I got > the same error at the same point "length(prlen) == 1 is not TRUE". > > 3. I googled for help, and found two e-mails that seemed connected to > what I was doing: > A. https://stat.ethz.ch/pipermail/bioconductor/2008-July/023668.html > B. http://article.gmane.org/gmane.science.biology.informatics .conductor/18963 > Because of these, I tried to read the .CEL files in using oligo > package, but that was also unsuccessful, because I couldn't build the > AffyGenePDInfoPkgSeed necessary for it. > > R version 2.12.1 (2010-12-16) > Copyright (C) 2010 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-pc-linux-gnu (64-bit) > >> library("pdInfoBuilder",lib.loc="/usr/local/lib/R/site-library") >> pgfFile<- "MoGene-1_0-st-v1.r4.pgf" >> clfFile<- "MoGene-1_0-st-v1.r4.clf" >> transFile<- "MoGene-1_0-st-v1.na31.mm8.transcript.csv" >> probeFile<- "MoGene-1_0-st-v1.probe.tab" >> pkg<- new("AffyGenePDInfoPkgSeed", author = "Emily Merrill", email = "deleted here", version = "0.0.1", genomebuild = "August 2010", biocViews = "AnnotationData", pgfFile = pgfFile, clfFile = clfFile, transFile = transFile, probeFile = probeFile) >> makePdInfoPackage(pkg,"/var/www/rdata/") > ====================================================================== > Building annotation package for Affymetrix Gene ST Array > PGF.........: MoGene-1_0-st-v1.r4.pgf > CLF.........: MoGene-1_0-st-v1.r4.clf > Probeset....: MoGene-1_0-st-v1.probe.tab > Transcript..: MoGene-1_0-st-v1.na31.mm8.transcript.csv > Core MPS....: coreMps > ====================================================================== > Parsing file: MoGene-1_0-st-v1.r4.pgf... OK > Parsing file: MoGene-1_0-st-v1.r4.clf... OK > Creating initial table for probes... OK > Creating dictionaries... OK > Parsing file: MoGene-1_0-st-v1.probe.tab... OK > Error in `[.data.frame`(probesets, , cols) : undefined columns selected > In addition: 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' > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >