Hello Francois, I have a little function that makes all possible contrasts between all the groups in your design matrix. Call it like this: contrast.matrix <- conMatrix(colnames(design)) conMatrix <- function(A) { N <- length(A) columns <- 0; for(i in 1:N) { columns <- columns + N - i} Acol <- c(" ") [rep(c(1), times=columns)] mat <- matrix(0, N, columns) k<-0 for(i in 1:N) { j <- 1 while( j <= N ) { if( j>i) { k <- k+1 Acol[k] <- paste(A[i],A[j],sep="-") mat[i,k] <- 1 mat[j,k] <- -1 } j <- j+1 } } rownames(mat) <- A colnames(mat) <- Acol mat } Let me know if you have any problems with it. Lynn Lynn Amon Research Scientist Dept of Pathology University of Washington lynnamon at u.washington.edu > Date: Sat, 11 Mar 2006 15:16:38 -0500 > From: Francois Pepin <fpepin at="" cs.mcgill.ca=""> > Subject: [BioC] automating makeContrasts call in limma > To: bioconductor at stat.math.ethz.ch > Message-ID: <1142108198.5347.78.camel at elm.mcb.mcgill.ca> > Content-Type: text/plain > > Hi everyone, > > is there a way to automate calls to makeContrasts? Right now, all the > contrasts have to be typed in or hard-coded. We're dealing with a couple > of hundreds of samples and it would make my life a lot easier if we > could generate everything automatically. I've looked briefly in the > archives but didn't find anything. > > Ideally, I would want to have a way to do: > > myContrasts<-c("t1-t2","t1-3","t2-t3") > contrast.matrix<-makeContrasts(myContrasts,levels=design) > > I haven't found a way to properly go around the 'substitute(list(...))' > call inside of makeContrasts. > > Right now, I'm writing code to output the proper call and copy/paste it > back in the console. > > Another alternative would be to create the contrast matrix myself. That > would be a more elegant way of doing it, but I don't quite feel > comfortable enough (yet) with design matrices for that. > > Francois >