[BioC] batch effect confounded with condition

[tefina]

I have 2 conditions (lets call them conditon A and B) with 3 biolog. replicates
each in batch 1.
Additionally, I have 2 other conditions (conditions C and D) with 3 biolog.
replicates in batch 2.

Questions of interest are: 
- diff. expr. genes between A vs B, and C vs D - this can be done via LIMMA
- common regulation of genes comparing AvsB and CvsD

Obviously, the second question is the more difficult one. At the moment, I would
just compare the lists of diff. expr. genes on the p-value level.