[BioC] Extract M values from probes set to cluster

[J.Oosting at lumc.nl]

As you can see from the dim() statements, the apply function has
transposed the array, you can correct that by transposing again.
Also you probably forgot the p.adjust() on the p-values from the linear
model.


M.ag<-t(apply(M.uw,1,function(x) (x[c(T,F)]+x[c(F,T)])/2))
MA.selected<-M.ag[selected,]


> 
> I try your suggestion and some errors appear.
> 
> Could you (or someone) help me again?
> 
> Thank you very much
> 
> > fit.2 <- eBayes(fit)
> > selected  <- (fit.2$p.value) <0.05
> >
> > selected[is.na(selected)]<-FALSE
> >
> > MA.selected <- MA.2$M[selected, ]
> >
> > M.uw<-unwrapdups(MA.2$M,ndups=2,spacing=32)
> >
> > M.ag<-apply(M.uw,1,function(x) (x[c(T,F)]+x[c(F,T)])/2)
> >
> > MA.selected<-M.ag[selected,]
> Error: (subscript) logical subscript too long
> > length(selected)
> [1] 3456
> > length(M.uw)
> [1] 20736
> > length(M.ag)
> [1] 10368
> > dim(MA.selected)
> [1] 2632    3
> > dim(M.uw)
> [1] 3456    6
> > dim(M.ag)
> [1]    3 3456
> >