[BioC] question regarding RMA on 2 different U133 platforms

[James W. MacDonald]

Hi James,

Were these chips run separately (e.g., at different times)? If so, you 
are much better off normalizing each group separately and then combining.

At about the same time that Affy started selling the U133-plus2 chip, 
they also started selling their own IVT kit, so it is possible that the 
133A chips were run using the Enzo IVT kit, and the 133-Plus2 chips were 
run using the Affy IVT kit. If this is true then you most certainly 
would not want to combine until after running RMA. And maybe not even 
then. In our experience, the batch effect tends to overwhelm any 
possible biological differences when trying to compare Affy and Enzo 
processed data.

Best,

Jim



On 8/14/2011 12:02 PM, James Anderson wrote:
> Hi,
>
> I have a bunch of cel files, part of them are in U133A, others are in
> U133plus2. Is there a way to RMA normalize them all together by only
> focusing on the common probe sets? or the RMA must be one in samples
> from each platform and think about a way to combine them?
>
> Thanks,
>
> -James
>
> [[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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