I am using limma to analyze my array data. In my dataset three contrasts are relevant, and limma is able to fit these in a single run. I now would like to use the package multtest to calculate adjusted p-values (note: i know limma also is able to calculate these but because of follow-up analyses i now prefer to do this through multtest). Using the function 'mt.rawp2adjp' I can obtain the adjusted p-values, but i have to run this function for each contrast seperately: res1 <- mt.rawp2adjp(fit2$p.value[,1], "BH") res2 <- mt.rawp2adjp(fit2$p.value[,2], "BH") res3 <- mt.rawp2adjp(fit2$p.value[,3], "BH") Since i would like to automate my script, i tried to run multtest with these arguments: res.ALL <- mt.rawp2adjp(fit2$p.value[,colnames(cont.matrix)], "BH") This function runs fine, but i end up with a single list with a length of 68070 entries (68070 = 3x 22690; the MOE430A affy array i use consists of 22690 probesets and i inputted in multtest 3 contrasts). Obviously, this is not the output i can use. Therefore i would appreciate to know whether multtest is able to handle multiple contrast in a single run, and if so, how to perform such analyses. TIA, Guido targets <- readTargets("targets_A23.txt") data <- ReadAffy(filenames=targets$FileName) eset <- rma(data) TS <- paste(targets$Strain, targets$Treatment, sep=".") TS <- factor(TS, levels=c("WT.Con","WT.WY","KO.Con","KO.WY")) design <- model.matrix(~0+TS) colnames(design) <- levels(TS) fit <- lmFit(eset, design) cont.matrix <- makeContrasts(WTwyvWTc=WT.WY-WT.Con, KOwyvKOc=KO.WY-KO.Con, Diff=(WT.WY-WT.Con)-(KO.WY-KO.Con), levels=design) fit2 <- contrasts.fit(fit, cont.matrix) fit2 <- eBayes(fit2) res1 <- mt.rawp2adjp(fit2$p.value[,1], "BH") adjp <- res1$adjp[order(res$index), ] etc ------------------------------------------------ Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> email: guido.hooiveld@wur.nl [[alternative HTML version deleted]]