[BioC] Bioconductor with Affymetrix Mouse Gene 1.0 ST

[M. Emily Merrill]

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"