[BioC] Bioconductor with Affymetrix Mouse Gene 1.0 ST

[cstrato]

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
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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'
>
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