Dear All,

I'am using limma package to extract the genes diffrentially expressed by 3
treatment,my database includes

48803 genes (rows) and 120 colones (40 replicates per treatment),my program
is as follows:

donne<-exprs(BSData.quantile)
groups<-as.factor(c(rep("Tem",40),rep("EarlyO",40),rep("LateO",40)))
design<-model.matrix(~0+groups)
colnames(design)=levels(groups)
fit<-lmFit(donne,design)
cont.matrix<-makeContrasts(TemvsEarlyO=Tem-EarlyO,TemvsLateO=Tem-LateO,EarlyOvsLateO=EarlyO-LateO,
levels=design)
fit2<-contrasts.fit(fit, cont.matrix)
ebfit<-eBayes(fit2)
gene1<-topTable(ebfit, coef=1)
gene2<-topTable(ebfit, coef=2)
gene3<-topTable(ebfit, coef=3)

results<-decideTests(ebfit) # I have a matrix that contains only 0 because

in the ligne 26  results <- new("TestResults", sign(tstat) * (p < p.value))
of decideTests program  the condition (p<p.value) is always false in my
case!!
something is wrong in my program, but I dont know where??

Any help would be appreciated.

Regards

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