Hi group,
I just got to know the error.
I am giving the colnames(design) after lmFit(eset,design).
If I interchange this.It works fine.
Thanks,
Viritha
On Thu, Apr 14, 2011 at 2:01 PM, viritha kaza <viritha.k@gmail.com> wrote:

> Hi group,
> I have a patient dataset of 6 control and 11 disease.
> so the code that I have written is:
>
> >library(affy)
> >library(limma)
> >eset<-as.matrix(read.table("GSEXXXX_series_matrix.txt",header = TRUE,sep =
> "\t", row.names = 1, as.is = TRUE)
> > design <- model.matrix(~-1 +
> factor(c(1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2)))
> > fit<-lmFit(eset,design)
> >colnames(design) <- c("CTR","DIS")
> >cont.matrix<-makeContrasts(DISvsCTR=DIS-CTR,levels=design)
> >fit<-contrasts.fit(fit,cont.matrix)
>
> # here I am getting the warning message:
> #In contrasts.fit(fit, cont.matrix) :  row names of contrasts don't match
> col names of coefficients.
>
> I guess this is because in my eset has 1st column row names.
> How do I accomodate that?
> Thanks,
> Viritha
>
>
>

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