[BioC] RMA vs gcRMA on 2 groups of samples

[Bogdan Tanasa]

Hi folks,

I would like to ask for your opinions on the following:

I have 60 expression profiles of 60 samples (cells and organs in
resting conditions).
I normalized these arrays in many ways, including RMA.

Considering the biological arguments (cells samples vs organs
samples), I am planning to do the normalization separately, on the
group of cell samples, and on the group of organ samples.

My questions are:

- after RMA normalization on separate groups of samples (cells vs
organs), the results are different, but are these better ? GO analysis
do not display major differences.

- would gcRMA work better than RMA ? The majority of opinions in SoCal
are pro-RMA.

thanks,

Bogdan