[R] filtering probesets with Bioconductor?

baumeist mark.baumeister7 at gmail.com
Tue Nov 22 23:51:57 CET 2011


I am relatively new to R and Bioconductor and am trying to filter the
topTable that I generated of differentially expressed genes from my
normlized eset file comprised of ~ 40 HG-133A Affy microarrays .  I would
like to see if particular probesets are represented in this list. 
Alternatively I would like to
generate a topTable of differentially expressed genes using only specified
probesets within my eset 

Can anyone tell me how I would  begin to approach this?  I have looked into
using the genefilter() function but can't figure out if it can take the
right parameters (i.e. specific probe set id's).

Thanks in advance,

This is the code I used to generate my topTable

> fit <- lmFit(eset, design)
> cont.matrix <- makeContrasts(NormalvsTumor=Tumor-Normal, levels=design)
> fit2 <- contrasts.fit(fit, cont.matrix)
> fit2 <- eBayes(fit2)
> topTable(fit2, number=100, adjust="BH") 

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