[BioC] Affy Gene ST arrays with "oligo"

[Cei Abreu-Goodger]

Hi all,

I've been trying to process a set of Affy MoGene-1_0-st-v1 CEL files 
with the "oligo" package. Using the "pd.mogene.1.0.st.v1" library, I can 
quite easily do read.celfiles followed by rma. But this library is built 
at the probeset level.

Does anyone have recommendations of how to end up working at the 
transcript level?

I thought I could simply build a new PdInfoPackage, using the transcript 
mapping file from Affy instead of the probeset, but that didn't seem to 
work (code below).

Many thanks,

Cei


library(AffyCompatible)
library(pdInfoBuilder)

seed <- new("AffyGenePDInfoPkgSeed",
     pgfFile = "MoGene-1_0-st-v1.r4.pgf", clfFile = 
"MoGene-1_0-st-v1.r4.clf",
     probeFile = "MoGene-1_0-st-v1.na28.mm9.transcript.csv",
     author = "Cei Abreu-Goodger",
     email = "cei at ebi.ac.uk", biocViews = "AnnotationData",
     genomebuild = "mm9",
     organism = "Mus musculus", species = "Mouse")

makePdInfoPackage(seed, destDir=".")


================================================================================
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.na28.mm9.transcript.csv
================================================================================
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.na28.mm9.transcript.csv ... OK
Error in `[.data.frame`(probesets, , cols) : undefined columns selected
In addition: Warning messages:


 > sessionInfo()
R version 2.9.0 (2009-04-17)
i386-apple-darwin8.11.1

locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] grid      stats     graphics  grDevices datasets  utils     methods
[8] base

other attached packages:
  [1] gplots_2.7.1              caTools_1.9
  [3] bitops_1.0-4.1            gdata_2.4.2
  [5] gtools_2.6.1              oligo_1.8.1
  [7] preprocessCore_1.6.0      pd.mogene.1.0.st.v1_0.0.1
  [9] oligoClasses_1.6.0        RSQLite_0.7-1
[11] DBI_0.2-4                 Biobase_2.4.1

loaded via a namespace (and not attached):
[1] affxparser_1.16.0 affyio_1.12.0     Biostrings_2.12.5 IRanges_1.2.2
[5] splines_2.9.0