On Dec 8, 2007 10:59 AM, James Anderson <janderson_net@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

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