[BioC] Limma and drug treatment

[Sean Davis]

>
> #Expression Set (exprSet) with
> #        571 genes
> #        94 samples
> #                 phenoData object with 18 variables and 94 cases
> #         varLabels
>
> ##Model Betabloc+Amines+Betabloc:Amines
> design<-model.matrix(~Betabloc*Amines-1,data=pData(clinicFull))
> fit <- lmFit(eset, design)
> eb<-ebayes(fit)
> topres<- 
> toptable(number=571,genelist=as.character(row.names(VD)),fit=fit,eb=
> eb,adjust="holm")
> length(which(topres$P.Value<0.01)

My guess is that your eb contains information for each of the  
coefficients.  You need to specify the coef parameter (1, 2, or 3) to  
get information about the other coefficients (the default coefficient  
is 1).  Along the same lines, if you do:

dim(eb$p.value)

my guess is that you have 3 columns.  Check to see if that is the case.

See the documentation for topTable for using the coef parameter.

> cont.matrix<-makeContrasts(Betabloc-Amines,levels=design)
> fit1<-contrasts.fit(fit,cont.matrix)
> eb1<-ebayes(fit1)
> topres1<- 
> toptable(number=571,genelist=as.character(row.names(VD)),fit=fit1,e
> b=eb1,adjust="holm")
> length(which(topres1$P.Value<0.01))
>

This looks right to me given what is above.

Sean