Hi. When I go through the limma examples with Hgu133plus2 data I can't get the M, A, and probe set IDs in the toptable result. my code below. data<-ReadAffy() eset<-rma(data) TS<-c("WT.U","WT.S","WT.U","WT.S","Mu.U","Mu.S","Mu.U","Mu.S","Mu.U"," Mu.S") TS<-factor<-factor(TS, levels=c("WT.U","WT.S","Mu.U","Mu.S")) design<-model.matrix(~0+TS) colnames(design)<-levels(TS) fit<-lmFit(eset, design) cont.matrix<-makeContrasts( WT.SvsU=WT.S-WT.U, Mu.SvsU=Mu.S-Mu.U, Diff=(Mu.S-Mu.U)-(WT.S-WT.U), levels=design) fit2<-contrasts.fit(fit, cont.matrix) fit2<-eBayes(fit2) toptable(fit2, coef=2, adjust.method="holm",number=10, sort.by="B") regards Anthony

>Date: Thu, 4 Nov 2004 15:18:17 +1100 (EST) >From: Anthony Bosco <unbelieve_04@yahoo.com.au> >Subject: [BioC] limma, TopTable help >To: bioconductor@stat.math.ethz.ch >Message-ID: <20041104041817.15180.qmail@web53708.mail.yahoo.com> >Content-Type: text/plain; charset=iso-8859-1 > >Hi. > >When I go through the limma examples with Hgu133plus2 >data I can't get the M, A, and probe set IDs in the >toptable result. That is because you are not using the same function as in the examples. Use topTable() not toptable(). When I updated the older functions lm.series(), ebayes() and toptable() to be more object-orientated, I kept the original function because some people prefer them for programming purposes. The newer more oop user- interface functions are lmFit(), eBayes() and topTable(). If you want all the bells and whistles of the examples, you must use these. Gordon >my code below. > >data<-ReadAffy() >eset<-rma(data) > >TS<-c("WT.U","WT.S","WT.U","WT.S","Mu.U","Mu.S","Mu.U","Mu.S","Mu.U", "Mu.S") >TS<-factor<-factor(TS, >levels=c("WT.U","WT.S","Mu.U","Mu.S")) >design<-model.matrix(~0+TS) >colnames(design)<-levels(TS) >fit<-lmFit(eset, design) > >cont.matrix<-makeContrasts( >WT.SvsU=WT.S-WT.U, >Mu.SvsU=Mu.S-Mu.U, >Diff=(Mu.S-Mu.U)-(WT.S-WT.U), >levels=design) > >fit2<-contrasts.fit(fit, cont.matrix) >fit2<-eBayes(fit2) > >toptable(fit2, coef=2, adjust.method="holm",number=10, >sort.by="B") > > > >regards > > >Anthony