[BioC] Filtering from Affy

[Michael Benjamin]

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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