[BioC] Combine affy ExpressionSets

[Wolfgang Huber]

Dear Kristian

I am afraid you will need to tell us more precisely what you mean by 
"combine", i.e. what is the goal or question behind it.

On a trivial level, of course you can combine the datasets, using 
"cbind", "merge" etc. However, there are many subtleties regarding 
normalisation (which first you should do separately for each array 
type), and batch effects. The appropriate solution, if any, will depend 
a lot on the nature and quality of your data, and your question.

	Best wishes
	Wolfgang


Unger, Kristian scripsit 01/21/2010 10:57 AM:
> Hi there!
> 
> I would like to combine different Affymetrix ExpressionSets.
> 
> Firstly I want to combine the esets of U133A and U133B chips from the samples. And if possible to do this I would like to combine that data set with data generated from U133Plus2 chips.
> 
> Is there a way to do this?
> 
> Best wishes
> 
> Kristian
> 
> _____
> 
> Dr Kristian Unger
> 
> Bioinformaticist Chernobyl Tissue Bank
> 
> Division of Surgery and Cancer
> 
> Imperial College London
> 
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> 
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> 
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> 
> Skype kristianunger
> 
> http://www1.imperial.ac.uk/medicine/about/divisions/is/histo/
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> 
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-- 

Best wishes
      Wolfgang


--
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber/contact