Respected Mam/Sir,,

I would like to know about design matrix and contrast, I have four CEL
files, two from wild type and two from mutant, each have two repliates. I
normalized the data,,  I have expression value in *dat.m*.
Now I consider differential expression

fit<-lmFit(dat.m, design)
fit<-eBayes(fit)
topTable(fit, coef=2)
tt<-toptable(fit, coef=2, n=nrow(dat.m))
rn<-rownames(tt)[tt$P.Value<-0.001]
I got only 127 genes

But i dont know how to work limma package, In my folder have four CEL files.
How to limma know about wild type and mutant cel files and how compare, that
i want to know ?
In above commands am not mention about cel files, which file is belong to
wild type & other..

How this package do work for 4 cel files???

Thanks & Regards
Varpall

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