[BioC] normalization between tissues

[Chun (Jimmie) Ye]

hey all,

i have several thousand affy arrays from various tissues and various  
mice...and we are doing a large scale eQTL study and i was wondering  
if anyone can suggest the best way to normalize/filter the data...i  
ran justRMA over all of the chips but we are only interested in the  
biologically active genes in each tissue type...i was thinking about  
doing a simple baseline filter on the RMA adjusted values for each  
tissue type...does that sound reasonable?

~j