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, Edmund

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. Sean

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