[BioC] Bioconductor with Affymetrix Mouse Gene 1.0 ST

[cstrato]

Dear Emily,

No, xps does not support gcrma() since I do not see any advantage 
compared to rma().

Best regards
Christian

On 3/25/11 10:34 PM, M. Emily Merrill wrote:
> 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"
>
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