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