[BioC] limma, TopTable help

[Gordon Smyth]

>Date: Thu, 4 Nov 2004 15:18:17 +1100 (EST)
>From: Anthony Bosco <unbelieve_04 at yahoo.com.au>
>Subject: [BioC] limma, TopTable help
>To: bioconductor at stat.math.ethz.ch
>Message-ID: <20041104041817.15180.qmail at web53708.mail.yahoo.com>
>Content-Type: text/plain; charset=iso-8859-1
>
>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.

That is because you are not using the same function as in the examples. Use 
topTable() not toptable().

When I updated the older functions lm.series(), ebayes() and toptable() to 
be more object-orientated, I kept the original function because some people 
prefer them for programming purposes. The newer more oop user-interface 
functions are lmFit(), eBayes() and topTable(). If you want all the bells 
and whistles of the examples, you must use these.

Gordon

>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