Normalizing multiple conditons all together

Question

[Raheleh]

Hello all,

I have expression profile of 5 different conditions with 2 different time point, all in one matrix.

I am using RMA to normalize them. Can I normalize them all together? or I have to normalize each condition with control group separately? If I normalize them all together don't I lose the biological differences? I searched but I couldn't find my answer.

I really appreciate any advice!