[BioC] Removing batch effects

[Aedin]

Dear BioC

I have a set of Affymetrix chips which have a clear "process day" batch
effect. This effect is only partially removed by RMA, gcRMA, vsn or
invariantset "expresso" normalisation. 

What would you recommend:

1. Normalize each small batch, merge the batches and re-normalize. If so
is one of the above normalisation options better than the options? 

2. Model the batch effect using fitPLM.  If so how to I extract the
"corrected" exprs?

3. Any other suggestions? 


Thanks a million for your help in this,

Aedin  Culhane