Hi all,

Can someone advise me as to whether or not it's acceptable to use  
different background subtraction methods (or normalization methods)  
for chips within the same marray object (i.e., set of experiments)?   
The reason I ask is that after normalizing my marrayRaw object with  
different background subtraction methods, I compute spatial- and  
intensity-dependent false discovery rates for the marrayNorm object.   
It seems reasonable to me to combine chips from marrayNorm objects  
after doing withinArrayNormalization and prior to doing  
betweenArrayNormalization in order to achieve lower FDRs.  Thoughts?

Cheers,

Jay Konieczka

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Jay H. Konieczka
Ph.D. Student, Antin Lab
Molecular & Cellular Biology
University of Arizona

Phone:  1.520.591.3446

1656 E. Mabel, MRB 317
Tucson, AZ 85724 USA
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