Hi Sergei,
You can't start a variable name with a number in R, so you can either
change to something like day.025, or you can construct your contrasts
matrix by hand, using something like
contrast <-
matrix(c(-1,0,0,1,0,0,0,-1,0,0,0,1,0,0,-1,0,0,0,0,1,0,-1,0,0,0,0,0,0,1
),
ncol=4, dimnames=list(colnames(design),
paste(colnames(design)[c(4:7)],
colnames(design)[1]))
I often construct the contrasts matrix by hand as it gives you more
control over the dimnames attribute.
Best,
Jim
BTW, you only need to send a question once. Sending it thrice may well
result in no response ;-D
Siarhei Manakou 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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