[BioC] Removing batch effects

Aedin aedin.culhane at ucd.ie
Mon Aug 22 22:47:29 CEST 2005


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



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