[BioC] automating makeContrasts call in limma

[Francois Pepin]

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