Combining multiple GSE datasets
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@luis-f-menezes-1651
Last seen 7.0 years ago
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.
GEOquery GEOquery • 1.6k views
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@christos-hatzis-2616
Last seen 7.0 years ago
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(eSet,eSet): Combine two eSet objects. To be combined, eSets must have identical numbers of featureNames, distinct sampleNames, and identical annotation. -Christos > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > LUIS F MENEZES > 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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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