[BioC] automating makeContrasts call in limm

[Gordon K Smyth]

> 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
>
> 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)

Your question isn't clear, at least not to me.  What is wrong with the code you've just given?

Is your question that you'd like to compute all pairwise comparisons between hundreds of different
treatments or patients?  If that is your real question, it might be best to tell us a little more
about your experiment.  It is easily done, but it doesn't sound necessarily very sensible.

Gordon

> 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