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Question: Is it possible to generate an ExpressionSet object that contain duplicate row names?
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gravatar for nqueralt@clinic.ub.es
6.2 years ago by
nqueralt@clinic.ub.es60 wrote:
Dear all, I am facing the problem that comes up when an ExpressionSet object is intended to be created parsing a matrix expression data with duplicate row names: > try(myExpressionSet <- new("ExpressionSet", exprs = myexprsunique, phenoData = myphenoData, annotation = myannotation, check.names=FALSE)) Error in data.frame(numeric(n), row.names = nms) : duplicate row.names: blu I was wondering if there exists a way to create this ExpressionSet object although duplicate row names exist in the expression matrix data parsed? Many thanks in advance. Kind regards, Núria [[alternative HTML version deleted]]
ADD COMMENTlink modified 6.2 years ago by Tim Triche4.2k • written 6.2 years ago by nqueralt@clinic.ub.es60
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gravatar for Tim Triche
6.2 years ago by
Tim Triche4.2k
United States
Tim Triche4.2k wrote:
rownames(myexprsunique) = make.unique(rownames(myexprsunique)) myExpressionSet <- new("ExpressionSet", exprs = myexprsunique, phenoData = myphenoData, annotation = myannotation) This is more of an R question than a BioC question, and don't forget to make the phenoData row names unique too. On Wed, Oct 12, 2011 at 11:59 PM, <nqueralt@clinic.ub.es> wrote: > Dear all, > > > > I am facing the problem that comes up when an ExpressionSet object is > intended to be created parsing a matrix expression data with duplicate row > names: > > > > > try(myExpressionSet <- new("ExpressionSet", exprs = myexprsunique, > phenoData = myphenoData, annotation = myannotation, check.names=FALSE)) > > Error in data.frame(numeric(n), row.names = nms) : > > duplicate row.names: blu > > > > I was wondering if there exists a way to create this ExpressionSet object > although duplicate row names exist in the expression matrix data parsed? > Many thanks in advance. > > > > Kind regards, > > > > Núria > > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]
ADD COMMENTlink written 6.2 years ago by Tim Triche4.2k
On 10/13/2011 01:52 AM, Tim Triche, Jr. wrote: > rownames(myexprsunique) = make.unique(rownames(myexprsunique)) > myExpressionSet<- new("ExpressionSet", exprs = myexprsunique, phenoData = > myphenoData, annotation = myannotation) > > This is more of an R question than a BioC question, and don't forget to make > the phenoData row names unique too. actually, Nuria was sent here from R-help ;) ExpressionSet row names are meant to be unique identifiers; store other identifiers in featureData, e.g., fData(myExpressionSet)[["MyIds"]] <- 'whatever' or create a featureData instance (it's an AnnotatedDataFrame, like phenoData) in new("ExpressionSet", featureData=featureData) Hope that helps, Martin > > > On Wed, Oct 12, 2011 at 11:59 PM,<nqueralt at="" clinic.ub.es=""> wrote: > >> Dear all, >> >> >> >> I am facing the problem that comes up when an ExpressionSet object is >> intended to be created parsing a matrix expression data with duplicate row >> names: >> >> >> >>> try(myExpressionSet<- new("ExpressionSet", exprs = myexprsunique, >> phenoData = myphenoData, annotation = myannotation, check.names=FALSE)) >> >> Error in data.frame(numeric(n), row.names = nms) : >> >> duplicate row.names: blu >> >> >> >> I was wondering if there exists a way to create this ExpressionSet object >> although duplicate row names exist in the expression matrix data parsed? >> Many thanks in advance. >> >> >> >> Kind regards, >> >> >> >> N?ria >> >> >> >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD REPLYlink written 6.2 years ago by Martin Morgan ♦♦ 21k
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