[BioC] using linear model of limma

[Jianping Jin]

Dear list:

A batch effect was observed in 16 out of 105 hgU133_plus2 arrays based on 
NUSE plot. I know SAM, like limma, is able to handle this kind of thing 
with setting block. But I am not sure if that is appropriate way for this 
unintentional situation.

I would try to use the lmFit function of limma with batch as a factor to 
remove the batch effect. Then use the resulting data values for other 
software applications, for example SAM. Here come my questions:
1. Should I apply the raw data, data at exprs, instead of eset at exprs for 
running lmFit?
2. If that is a right way, how can I extract the lmFit normalized data for 
next RMA or GCRMA?

Please point it out if I am confused with something! I will appreciate your 
help!

Jianping

##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104
University of Chapel Hill
Chapel Hill, NC 27599
Phone: (919)843-6105
FAX:   (919)843-3103
E-Mail: jjin at email.unc.edu