[BioC] help with using pdInfoBuilder and oligo for Affy Gene Set arrays

[James W. MacDonald]

Hi Mark,

Mark Kimpel wrote:
> I have followed Jim's advice (
> http://thread.gmane.org/gmane.science.biology.informatics.conductor/18959/focus=18963)
> and built, without error messages, the pdInfo package for Affy Rat
> Gene
> ST. Now I am stuck. I've read the oligo vignette and it doesn't really
> address non-SNP arrays, particularly how to make an affyBatch for further
> processing. Can someone point me to the relevant info?

?read.celfiles
?rma

Note that there isn't an AffyBatch class in oligo. You will be using an 
ExpressionSet for raw data and an ExonFeatureSet for the expression values.

Best,

Jim


> Mark
> ------------------------------------------------------------
> Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
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-- 
James W. MacDonald, M.S.
Biostatistician
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