[BioC] design matrix with limma

[James MacDonald]

-- 

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


>>> Diya v <diya_2208 at yahoo.co.in> wrote:
> Hi,
> 
> I have a question.I have 2control samples(v7,v8) and 2 treatment
> samples(g1,g4).I have the data generated from aroma.affymetrix and I
> have applied log2 on it and load the data for doing statistical
> analysis by limma.Is my design matrix correct?

Yes.

Best,

Jim


> 
> dat.m<-read.csv("datam.csv",skip=0)
> genes<-rownames(dat.m)
> groups<-c(C,C,T,T)
> groups<-as.factor(groups)
> design<-model.matrix(~groups)
> design
> fit<-lmFit(dat.m, design)
> fit<-eBayes(fit)
> toptable(fit, coef=2)
> 
> Thanks,
> Diya
> 
> 
> 
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