[BioC] subsetting in limma

echang4@life.uiuc.edu echang4 at life.uiuc.edu
Tue Jan 24 05:44:59 CET 2006

Hi Bioconductor users,
This is a very naive question on exporting subsets in limma.  But I am not
very familiar with pogramming.

I am trying to work through the limma user guide Sec 8.8 "Time Course
Experiments". I am able to complete the limma analysis but I am stuck
after subsetting the genes to only include genes with adj. p values < 0.05

> fit2 = contrasts.fit(fit, cont.matrix)
> fit2 = eBayes(fit2)
> results2 <- decideTests(fit2)
> selected.wt<- p.adjust(fit2$F.p.value, method="fdr") < 0.05

My question is how do I export the genes names in "selected.wt" out as a
text file?
I tried
> write.csv(selected.wt, "selected.wt.csv")
but I get a single column with TRUE and FALSE.

Thank you very much,

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