Thanks Sean Davis for your reply. Yes. I know that #1 = #4 and and #2=#3. I mentioned the 4 categories to clarify the question. Here is the code that I wrote: dge.list <- estimateTagwiseDisp(dge.list, prior.df=50) #estimate tagwise dispersion de.exactTest.tgw <- exactTest(dge.list, dispersion = "tagwise", pair = c("A", "B")) resultsTbl.tgw <- topTags(de.exactTest.tgw, n = nrow(de.exactTest.tgw$table))$table summary( decideTestsDGE( de.exactTest.tgw , p.value = 0.05 ) ) the summary function will show the following outputs: [,1] -1 207 0 8394 1 359 Based on the documentation, I think that these 207 are upregulated in A. The 359 genes are upregulated in B .. corrrect? Now, I want to get the genes of the two groups (207 and 359) and print each gene set in a file. In the past couple of hours, I tried to write it as: rownames(de.exactTest.tgw[decideTestsDGE( de.exactTest.tgw , p.value = 0.05 ) == 1]$table) #show the 359 genes rownames(de.exactTest.tgw[decideTestsDGE( de.exactTest.tgw , p.value = 0.05 ) == -1]$table) #show the 207 genes I hope this was correct? I am wondering if there is a quick way to remove the double-quotation from the outputs of previous commands and write it one gene per line to file Regards, On Sat, Apr 13, 2013 at 12:30 AM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Fri, Apr 12, 2013 at 4:50 PM, Abdullah khamis > <abdullahkhamis@gmail.com> wrote: > > Dear edgeR Community, > > > > I have 12 samples that belong to two groups (A and B), 6 samples per > group, > > and I want to know which genes are up-regulated in group A and > > down-regulated in B and vice versa. > > I use the functions summary() and the function decideTestsDGE() but I > could > > not get the summary information about > > 1) up-regulated genes in Group A > > 2) down-regulated genes in Group A > > 3) up-regulated genes in Group B > > 4) down-regulated genes in Group B > > Hi, Abdullah. > > You might need to show us what you have tried. Keep in mind that > genes in #1 above are the same as genes in #4 and that genes in #2 are > the same as #3 when you have two groups. > > Sean > [[alternative HTML version deleted]]