[BioC] how to do with global shift

[Dapeng Cui]

Dear Bioconductor users,

Firstly I'm sorry if this subject is appropriate for the list. I remember there
were some discussion in this list on what to do when treatment produces a
global shift on gene expression.  Now I'm facing this problem on T cell
activation experiment. Upon activation T cells change dramaticaly. They start
proliferation, getting much bigger and make more RNA. After running affy chips,
whatever normalizations I did, thousands genes(20%~30%) on chip changed. Of
course they all give equal number of up- and down-regulated genes. I feel
really hard to make explantation from these data. And I think it's dangerous to
normalize using housekeeping genes because HKs also change after T cell
activation. Could anybody please give me some clues/publications on which
pre-process/normalization works better for this situation?


-- 
Dapeng Cui
Department of Medicine
Emory University School of Medicine
Atlanta, GA 30322