[BioC] automating makeContrasts call in limma

[Greg Finak]

The following line should do what you want.

> myContrasts<-c("t1-t2","t1-3","t2-t3")
contrast.matrix <- eval(as.call(c(as.symbol("makeContrasts"),as.list 
(myContrasts),levels=list(design))))

It's the same convention as making calls to R functions through C code.

Cheers,


On 11-Mar-06, at 3:16 PM, Francois Pepin wrote:

> 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
>
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Greg Finak
PhD Candidate
McGill Center For Bioinformatics
(W)(514)398-7071 x09317
finak at mcb.mcgill.ca