Hi, thanks to Rafael and Deepayan I am a little closer to the end but I still= =20 dont get the identification of the probes differentially expressed using th= e=20 following with multtest and the doc from the package (I am just following t= he=20 whole procedure form the documentation of the package using my data from 2= =20 duplicated experiments I want to compare, there might be optimization for t= he=20 kind of test to use etc but this is not my purpose right now). Here is the= =20 procedure and the problem at the end: library(multtest) library(affy) data<-ReadAffy() data2<-rma(data) save(data2, file=3D"cwcneo0A.txt")=A0=A0 -> shall I rename it in a differen= t way=20 using a .rda instead of the .txt ? class<- c(0,0,1,1)=20 teststat<-mt.teststat(exprs(data2),class) postscript("mtQQ.eps") qqnorm(teststat) qqline(teststat) dev.off() pdf("mtQQ.pdf") qqnorm(teststat) qqline(teststat) dev.off() tmp<- mt.teststat.num.denum(exprs(data2),class,test=3D"t") num<- tmp$teststat.num denum<- tmp$teststat.denum postscript("mtNumDen.eps") plot(sqrt(denum), num) dev.off() pdf("mtNumDen.pdf") plot(sqrt(denum), num) dev.off() rawp0 <- 2 * (1-pnorm(abs(teststat))) procs<- c("Bonferroni", "Holm", "Hochberg", "SidakSS", "SidakSD", "BH", "BY= ") res <- mt.rawp2adjp(rawp0, procs) adjp <- res$adjp[order(res$index), ] round(adjp[1:10, ], 2) resT <- mt.maxT(exprs(data2), class, B=3D1000) ord <- order(resT$index) rawp <- resT$rawp[ord] maxT <- resT$adjp[ord] teststat <- resT$teststat[ord] mt.reject(cbind(rawp, maxT), seq(0, 1, 0.1))$r which <- mt.reject(cbind(rawp, maxT), 0.01)$which[ ,2] Here I am and if I do:=20 geneNames(data2) I get all the probe sets, same with rownames(exprs(data2)) but I just like to have the one identify and "collected" in which ! Thanks for any help Philippe=20 [[alternate HTML version deleted]]