[BioC] Extract M values from probes set to cluster

[Sean Davis]

On Tuesday 13 February 2007 06:51, Marcelo Laia wrote:
> Dear Sean
>
> I thought that I did a mistake in selected. Then, I try... But no success.
>
> Here are the outputs:
> > selected  <- p.adjust(fit.2$p.value) <0.05
> > summary(selected)
>
> Mode   FALSE    TRUE    NA's
> logical    2565     130     761
>
> > length(selected)
>
> [1] 3456
>
> > MA.selected <- MA.2$M[selected, ]
> > dim(MA.selected)
>
> [1] 1782    3
>
> I thought that I did a mistake here:
> > selected  <- p.adjust(fit.2$p.value) <0.05
>
>                       ^^^^^^^^^^
>
> > selected  <- (fit.2$p.value) <0.05
> > length(selected)
>
> [1] 3456
>
> > MA.selected <- MA.2$M[selected, ]
> > dim(MA.selected)
>
> [1] 4154    3
>
> > fit.2 <- eBayes(fit)
>
> Thank you very much

Looks like your fit.2$p.value is shorter than the MA.2 object, so you will 
need to go about things a different way.  I typically use topTable like:

tt <- topTable(fit2)
heatmap(MA.2$M[as.numeric(rownames(tt)),])

Of course, you can make any call to topTable you like.

Does this work for you?

Sean