[BioC] limma, TopTable help

[Anthony Bosco]

Hi.

When I go through the limma examples with Hgu133plus2
data I can't get the M, A, and probe set IDs in the
toptable result.

my code below.

data<-ReadAffy()
eset<-rma(data)

TS<-c("WT.U","WT.S","WT.U","WT.S","Mu.U","Mu.S","Mu.U","Mu.S","Mu.U","Mu.S")
TS<-factor<-factor(TS,
levels=c("WT.U","WT.S","Mu.U","Mu.S"))
design<-model.matrix(~0+TS)
colnames(design)<-levels(TS)
fit<-lmFit(eset, design)

cont.matrix<-makeContrasts(
WT.SvsU=WT.S-WT.U,
Mu.SvsU=Mu.S-Mu.U,
Diff=(Mu.S-Mu.U)-(WT.S-WT.U),
levels=design)

fit2<-contrasts.fit(fit, cont.matrix)
fit2<-eBayes(fit2)

toptable(fit2, coef=2, adjust.method="holm",number=10,
sort.by="B")



regards


Anthony