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 [[alternate HTML version deleted]]

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 > > [[alternate HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >