Hi Sergei,

I am very new to BioConductor so I could be wrong about this, but I think
that your problem is the fact that your levels start with numbers.
Why don't you try putting a letter or a dot in front of each level and see
if it works then.

Something like this:

> contr_matrix<-makeContrasts
>
> (.1days-.025days, .2days-.025days, .4days-.025days,. 8days-.025days,
> .12days-.025days, .16days-.025days, levels=design)


If this is the case you'll probably have to rename the columns on your
design too.

Cheers,

Artur

On Wed, 4 Jul 2007 14:16:38 UT, Siarhei Manakou <sm7@sanger.ac.uk> wrote:
>
> Hello,
>
> Im a first year PhD student in Sanger institute - just started working
> with bioconductor and encoutered problem while building a contrast matrix. I
> first made  the desing matrix:
>
> > design<-model.matrix(~-1 + pData(eset)$days)
> > colnames(design)<-levels(pData(eset)$days)
> > colnames(design)
> [1] "025days" "12days"  "16days"  "1days"   "2days"   "4days"   "8days"
>
>
> Then attempted to make a contrast matrix:
>
> > contr_matrix<-makeContrasts(1days-025days, 2days-025days, 4days-025days,
> 8days-025days, 12days-025days, 16days-025days, levels=design)
>
> but it produces the following error message:
>
> Error: syntax error, unexpected SYMBOL, expecting ',' in
> "contr_matrix<-makeContrasts(1days"
>
> I would be very grateful if somebody could point out what the problem
> could be. I am using R-2.5.0 under Linux.
>
> Thanks a lot!
> Sergei
>
>
>
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