[BioC] Combining two datasets - help to use GeneMeta.

Robert Gentleman rgentlem at fhcrc.org
Sun Jun 11 20:23:53 CEST 2006

Sean Davis wrote:
> Sharon wrote:
>> Hi,
>> I am trying to combine two Affy datasets (on rae230a chips), where
>> experiments done one year apart. In the first dataset, we have 2
>> strains with each strain treated and untreated.  But for the second
>> dataset, we have just 2 strains untreated.
>> Because of unequal levels in the 2 datasets, I am not able to use
>> 'getdF'  in GeneMeta as it is.  Any suggestions for using 'getdF' for
>> this situation?  or any alternate way of combining these 2 datasets?
> Are these datasets really that much different that you can't just 
> combine them?  They may be, but have you looked at affyPLM results, 
> density plots, etc., just to be sure?  If they aren't that much 
> different, perhaps you can just normalize them together and move on? 
> Just asking....

  Sorry, but that is, IMHO, a bad idea. You should never jointly 
normalize separate experiments. Normalize separately and use a random 
effects model for the experiments. As, for how to handle different 
levels of factors/covariates, the issue then becomes one of what can be 
estimated from both. Once you identify that you can set up the 
appropriate model and then use tools like nlme and lmer (depending on 
the model) to estimate parameters. But this will require some 
statistical expertise and for that you will have to look locally, these 
things are too hard to do over the internet,  IMHO.
  There is a BioC technical report on Synthesis of microarray 
experiments that outlines some of these details more completely.

  best wishes

> Sean
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Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org

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