[BioC] Batch effects and linear models

[Fangxin Hong]

>>From my numeralogist roots, I know that a mixed model across all arrays
>> need not give the same estimates as a linear model of the residuals from
>> linear models derived for each lab. Any pointer on how other people
>> handle batch effects would be most useful and most welcome.
If I use linear model. I would normalize all arrays (from boht labs)
together and include "batch" effect as one factor in the linear model.
If only identifying differentially expressed genes between two conditions,
there is a method called "rank product" can handle this situation (two lab
data) directly.


Hopefully this helps.
Fangxin


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-- 
Fangxin Hong, Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu