[BioC] combining different type affy chip data

[James W. MacDonald]

Yanqin Yang wrote:
> Hello,
> 
> Does anyone  know how to combine data sets derived from two different
> affy mouse genome sets (U74 and MOE430_2) for data analysis? For
> example, similar condition samples are hybridized with two types affy
> chips. Is it possible to do normalization crossing different type
> affy chips? Thanks!

You would have to look it up, but I think the mouse4302 chip is based on 
newer annotation than the mgu74a. Anyway, there are only 43 overlapping 
probeset IDs (all AFFX-type control sequences), so there is no simple 
way to combine the two chip types.

This technical issue aside, I don't think it would be a good idea 
anyway. I would have to imagine that the two chip types were run at very 
different times, and possibly by different people. This alone may 
introduce large batch effects that would make normalization together a 
Bad Idea.

A better idea would be to normalize the data sets separately, and then 
use something like MergeMaid to find common genes between the two data 
sets, and then possibly something like GeneMeta to fit a mixed model.

Best,

Jim


> 
> Yanqin
> 
>  ---------------------------------
> 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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