[BioC] Filtering from Affy

[Rafael A. Irizarry]

i highly recommend learning about the exprSet class and in 
particluar the phenoData slot. a place to start is the 
vignette for the Biobase package. Bioconductor also has a genefilter 
package that you might find useful.

hope this helps,
-rafael

On Wed, 11 Dec 2002, 
Michael Benjamin wrote:

> Hello-
>  
> I have Affymetrix .cel files that I have read into R using the affy
> package.  I am able to do normalization, transformation, and even
> cluster analysis.  I cannot figure out how to do gene filtering
> operations-how do I tell R which samples I am interested in comparing to
> which other samples?  I have two duplicate experiments that are vector
> controls, two duplicate experiments that are virally transfected, and
> one experiment that is the parental cell line.  How do I compare
> differential gene expression between the vector controls and the virally
> transfected cell lines, for example?
>  
> Thanks,
> Michael Benjamin, MD
> 
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