[BioC] scale between two independent arrays

[Weiwei Shi]

Hi, there:

I am using two microarray datasets (both are on the same platform,
U133A). I build a predictive model from one dataset and validate the
model on another. My aim is to test my methodology's performance on
cross-lab situation.

I notice the log2intensity are a little bit different between the two
arrays (the two arrays are done in two different labs and happen to
have some same clinical class label). I use generic scale function in
R to "normalize" them. I am wondering if it is appropriate and if
there are other approaches for that.

Thanks,
-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

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