Duplicated Gene IDs - averaging
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@maciej-jonczyk-3945
Last seen 7.1 years ago
Dear List Members, I have problem with ExpressionSet object. I've constructed such an object with data with duplicated gene Ids (after assigment of probes IDs to genes). I know that ExpressionSet doesn't support such a situation, but I've thought that function poe.mcmc from metaArray package will handle it without problems - unfortunately, after few hours of computing I've had an error. So I'd like to ask how can I compute an average or -better- median for duplicated IDs in exprs() slot in ExpressionSet object. Or just for matrix, so I could set it as an exprs(). I suspect it's basic function in R, but I've spent all day searching it and I haven't succeeded. I'd also prefer not to convert ExpressionSet to another data type (e.g. MAList, RGList) in order to perform such an operation. Any help will be valuable, Best Regards -- Maciej Jonczyk, Department of Plant Molecular Ecophysiology Institute of Plant Experimental Biology Faculty of Biology, University of Warsaw 02-096 Warszawa, Miecznikowa 1 -- This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com
convert metaArray convert metaArray • 3.5k views
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Aleš Maver ▴ 80
@ales-maver-3556
Last seen 7.1 years ago
Dear Maciej, are you perhaps looking for the aggregate function, such as in example below? #Generate matrix with duplicated row names mat<-matrix(rnorm(60), nrow=12) row.names(mat)<-rep(letters[1:c(nrow(mat)/3)], each=3) # Merge rows in matrix using median aggregate(mat, by=list(row.names(mat)), FUN=median) Hope it helps! Ales 2011/9/25 mjonczyk <mjonczyk@biol.uw.edu.pl> > Dear List Members, > > I have problem with ExpressionSet object. I've constructed such an object > with data with > duplicated gene Ids (after assigment of probes IDs to genes). > I know that ExpressionSet doesn't support such a situation, but I've > thought that function > poe.mcmc from metaArray package will handle it without problems - > unfortunately, > after few hours of computing I've had an error. > > So I'd like to ask how can I compute an average or -better- median for > duplicated IDs in > exprs() slot in ExpressionSet object. Or just for matrix, so I could set it > as an exprs(). > I suspect it's basic function in R, but I've spent all day searching it and > I haven't succeeded. > I'd also prefer not to convert ExpressionSet to another data type (e.g. > MAList, RGList) > in order to perform such an operation. > > Any help will be valuable, > Best Regards > > -- > Maciej Jonczyk, > Department of Plant Molecular Ecophysiology > Institute of Plant Experimental Biology > Faculty of Biology, University of Warsaw > 02-096 Warszawa, Miecznikowa 1 > > > > -- > This email was Anti Virus checked by Astaro Security Gateway. > http://www.astaro.com > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > -- Aleš Maver Ales.Maver@gmail.com [[alternative HTML version deleted]]
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@maciej-jonczyk-3945
Last seen 7.1 years ago
Dear Ales, thanks a lot for your very quick help. It is exactly what I needed! Best Wishes, Maciej > # Merge rows in matrix using median > aggregate(mat, by=list(row.names(mat)), FUN=median) > > Hope it helps! > Ales > -- Maciej Jonczyk, Department of Plant Molecular Ecophysiology Institute of Plant Experimental Biology Faculty of Biology, University of Warsaw 02-096 Warszawa, Miecznikowa 1 -- This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com
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