[BioC] Query regarding limma package

[James W. MacDonald]

Hi Varpal,

varpal singh wrote:
> 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..

I think the Limma User's Guide covers this quite extensively. You can 
read it using

limmaUsersGuide()

Best,

Jim


> 
> How this package do work for 4 cel files???
> 
> Thanks & Regards
> Varpall
> 
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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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