[BioC] limma and 2-array divided probe sets

[Jorrit Boekel]

Dear list,

I would like to do an analysis on a published dataset that used the 
"previous generation" (quote Affy) arrays Mu11K. These contain ~11K 
probes divided over 2 chips, give rise to 2 cel files, and use different 
annotation packages.

As I am no limma-veteran, I wondered if there was a way to concatenate 
the data from these files before or after reading it into limma as two 
separate affybatch objects, and then make an eSet. If not, should I 
instead analyse the chips separately and merge the resulting toptables?

cheers,
-- 
Jorrit Boekel
Ph.D. student
Dept. of Neuroscience
Karolinska Institute
Stockholm, Sweden