[BioC] about microarray batch effect and treatment effect

[aedin culhane]

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