[BioC] batch effect confounded with condition

[tefina]

Thanks for all your answers.

I think I will pursue the following strategy:
I will analyse each experiment separately. Contrasts within each experiment
should be fine. (As batch 1 concerns only experiment 1 and batch 2 concerns only
experiment 2).
Any comparisons between experiments ( = comparisons between batches) I will only
do on the p value level. So I will only evaluate things like: do genes that show
up in experiment 1 also show up in experiment 2?

Doing this, I should be more or less on the safe side.
What do you think?