[BioC] subsetting in limma

Sean Davis sdavis2 at mail.nih.gov
Wed Jan 25 12:55:53 CET 2006

On 1/23/06 11:44 PM, "echang4 at life.uiuc.edu" <echang4 at life.uiuc.edu> wrote:

> 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?

You might want to look at ?write.fit.


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