>Date: Thu, 14 Apr 2005 15:07:56 -0300 >From: Marcelo Luiz de Laia <mlaia@fcav.unesp.br> >Subject: [BioC] How extract F.p.value and lods values from a eBayes > object in limma??? >To: bioconductor@stat.math.ethz.ch > >Hi, > >I do the commands: > >todos20050401.fit3 <- eBayes(todos20050401.fit2) >selected <- p.adjust(todos20050401.fit3$F.p.value,method="fdr")<0.05 >selected.result <- todos20050401.fit3$genes[selected,] >write.table(selected.result,"selected.F.p.value0.05.csv",sep=",") > >In my cvs file I get the name of genes, but I don t get the "F.p.value" >nor "lods" values. You've asked for the names of the genes with small values of F.p.value, and that's what you got. >I try: > >todos20050401.fit3$genes[selected,],todos20050401.fit3$F.p.value,todo s20050401.fit3$lods > > >Error: syntax error > >I read about cbind, but I don t obtain success, too. > >Please, Anyone point me if is possible todo? The answer to the question in the title of your email is: todos20050401.fit3$F.p.value and todos20050401.fit3$lods What is it that you really want? Gordon >Thanks > >Marcelo

Dear Mr Smyth, I am sorry, but I dont was clear in my subject question. I try to modify the subject now, to adjust it, but I was not capable to become it more clearly. Please, my excuses! I obtained to extract the individual values, but I would like to get them in an only table or archive together. I obtain to have the significant genes, but I would like to have to see the significant genes in a column and, to the side of them, the values of "F.p.values" and "lods", respectively. For example: Genes F.p.value lods 1 0.001 -y 200 0.002 x 301 0.040 k . . . Mrcelo Gordon Smyth disse: > >>todos20050401.fit3$genes[selected,],todos20050401.fit3$F.p.value,tod os20050401.fit3$lods > The answer to the question in the title of your email is: > > todos20050401.fit3$F.p.value > > and > > todos20050401.fit3$lods > > What is it that you really want? > > Gordon