[BioC] normalize by or across all treatments

[Leanna House]

In replicates of 3, I have a set of control and 4 treatment arrays.  My
question is, do I normalize (via rma) using all of the arrays at once, or
do I normalize by treatment.  I have asked other reliable sources and have
received conflicting responses.  I feel the issue is that, in one case, I
may, if not completely wipe out, severely diminish any possible treatment
effects, whereas, in the other case, I may actually induce a treatment
effect.  Any thoughts?

Thank you so much,
Leanna