[BioC] Combining multiple GSE datasets

Christos Hatzis christos.hatzis at nuverabio.com
Fri Jan 25 19:03:37 CET 2008

There is a combine method for eSets.  So if you have your datasets already
as eSets, it would be as simple as

combined.eset <- combine(eset1, eset2)

And you can use this recursively for more than two esets.

Beware of some constraints though.  From the documentation for eSet:

	Combine two eSet objects. To be combined, eSets must have identical
numbers of featureNames, distinct 	sampleNames, and identical

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch 
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
> Sent: Friday, January 25, 2008 12:38 PM
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Combining multiple GSE datasets
> Hello.
> I have imported several (35) GSE datasets (many from 
> different platforms, but all from the same species) using 
> GEOquery. I want to combine them into one large dataframe 
> containing the genes that are represented in all the arrays. 
> Is there any package that would do this automatically? If 
> not, does anyone have any suggestions?
> Thank you.
> Luis.
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