Dear Sean I have used combat (available as an R script) from Evan Johnson and Cheng li with good success for removing batch effects. I can send you the script. I have edited it so that it work a little better with BioC. Aedin On Dec 8, 2007 10:59 AM, James Anderson <janderson_net at="" yahoo.com=""> wrote: Dear List, I am now analyzing some Affy data with obvious batch effect with different dose level, one conceptual question regarding batch effect and treatment effect is that does the batch effect affect control or treated samples differently? You could fit a linear model that includes treatment effect, batch effect, and an interaction effect. Sean