[BioC] Bioconductor with Affymetrix Mouse Gene 1.0 ST

[M. Emily Merrill]

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'