[BioC] How to pool subgroups for makeContrasts() and subsequent limma analysis?

[René]

Dear all,

As I am still stuck on this topic, I would like to ask whether it is OK to 
completely replace the comparison (B1+B2+B3)/3 - A by a separate run of B-A in 
order to obtain some meaningful results. By heart I would say that this is not 
the case, as it would mean combining two independent design matrices and 
therefore two different models. Nevertheless, I am running out of ideas on how 
to perform this analysis and I would like to finish it by the end of February.

Any recommendations are more than welcome.

Best regards