[BioC] GCRMA question

[Radu Dobrin]

Dear all,

I have been using GCRMA for the last month or so, jumping from AFFY MAS5 
since everybody agreed GCRMA is better. Now I am having some doubts 
about the way to use it. It was not clear to me from the beginning if I 
could normalize all the data from different treatments at once or that I 
would have to treat separately the repeats. MAS5 is one chip at a time 
(no linear model). How do you use GCRMA? In my case I have 7/7/2 repeats 
for 3  different "treatments" (cell populations sorted in different 
ways). How should I proceed? Also what if I don't have any repeats and 
only one chip for each "treatment"?.

Until now I have loaded all A chips and GCRMA all of them together.

Thanks for helping,
Radu

-- 
Dr. Radu Dobrin
Department of Molecular Biology
Princeton University
Washington Road
Princeton, NJ 08544-1014
Phone: 609-258-5657
E-mail: rdobrin at molbio.princeton.edu