Hi, I ve been trying to use edgeR for RNA-Seq Dierential Expression and I am trying to use in R the plotMDS function but I get the following cryptic error message > plotMDS( cds , main = "MDS Plot for Count Data", labels = colnames( cds$counts )) Error in cmdscale(as.dist(dd), k = ndim) : 'k' must be in {1, 2, .. n - 1} Would any of you have an idea what this error mean. Thanks for your help Best regards Nicolas [[alternative HTML version deleted]]

Hi Nicolas, What is your input "cds"? The input should be matrix, or "any data object which can be coerced to a matrix, such as ExpressionSet or EList". Di ---- Di Wu Postdoctoral fellow Harvard University, Statistics Department Harvard Medical School Science Center, 1 Oxford Street, Cambridge, MA 02138-2901 USA ________________________________________ From: bioconductor-bounces@r-project.org [bioconductor- bounces@r-project.org] On Behalf Of Nicolas Devos [nicolasdevos@mac.com] Sent: Wednesday, November 14, 2012 5:37 PM To: bioconductor at r-project.org Subject: [BioC] plotMDS error Hi, I ve been trying to use edgeR for RNA-Seq Dierential Expression and I am trying to use in R the plotMDS function but I get the following cryptic error message > plotMDS( cds , main = "MDS Plot for Count Data", labels = colnames( cds$counts )) Error in cmdscale(as.dist(dd), k = ndim) : 'k' must be in {1, 2, .. n - 1} Would any of you have an idea what this error mean. Thanks for your help Best regards Nicolas [[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

Hi, On Wed, Nov 14, 2012 at 5:37 PM, Nicolas Devos <nicolasdevos at="" mac.com=""> wrote: > Hi, > > I ve been trying to use edgeR for RNA-Seq Dierential Expression and I am trying to use in R the plotMDS function but I get the following cryptic error message > >> plotMDS( cds , main = "MDS Plot for Count Data", labels = colnames( cds$counts )) > Error in cmdscale(as.dist(dd), k = ndim) : > 'k' must be in {1, 2, .. n - 1} > > Would any of you have an idea what this error mean. Could you provide the output of `class(cds)` and `sessionInfo()`, please? Thanks, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact