[BioC] Another limma factorial that needs controlling and pairing

[sabrina]

Hi, Karl:
I have a similar question as yours, did you figure it out since your last post?

Other question I have is about using topTable. In your previous
design, did you use topTable for each contrast, meaning for each particular
contrast, how you find the top list of genes? If that is the case, what is the
best way to sort the genes? Did you use B value or adj.p? Or you just used
decideTests? 

Thanks

Sabrina