You need makeContrasts(contrasts=con, levels=dMatrix) See the help page. Gordon >Date: Thu, 25 Oct 2007 12:46:57 +0200 >From: Amin Moghaddasi <a.moghaddasi at="" gmail.com=""> >Subject: [BioC] automating makeContrasts call in limma >To: bioconductor at stat.math.ethz.ch > >Hi list, > >I am trying to call makeContrasts() in limma to accept character vector >of all samples vs control. But it seems that makeContrasts() consider >only the first element in the contrast vector. > >Basically what I've done is first to assign design matrix "dMatrix", >then make a contrast character vector "con" using paste() like: > > > dMatrix <- model.matrix(~ -1+factor(c(1,1,2,2,3,3))) > > colnames(dMatrix) <- paste("s", 1:(dim(dMatrix)[2]), sep = "") > > con<-paste(rep('s'),sep="",3:1,"-s1") > > con >[1] "s3-s1" "s2-s1" "s1-s1" > >Then call makeContrasts like: > > cMatrix <- makeContrasts(con, levels=dMatrix) > > cMatrix > Contrasts >Levels s3-s1 > s1 0 > s2 0 > s3 0 > >The expected result is : > > cMatrix <- makeContrasts("s3-s1","s2-s1","s1-s1", levels=dMatrix) > > cMatrix > Contrasts >Levels s3-s1 s2-s1 s1-s1 > s1 -1 -1 0 > s2 0 1 0 > s3 1 0 0 > >So any advise of what I'm doing wrong would be appreciated, Or how can I >automatically call makeContrasts using a vector of all samples vs >control. > >Thanks in advance, >Amin.