Dear Gordon, Thanks for your input on plotMDS. Can you please comment on the second question I had - is it possible to use the DGEList object to make a 3D PCA plot? Thanks, Manoj. ________________________________ From: Gordon K Smyth <smyth@wehi.edu.au> Cc: Bioconductor mailing list <bioconductor@r-project.org> Sent: Wednesday, May 22, 2013 4:53 PM Subject: edgeR MDS Dear Manoj, plotMDS does not do PCA.  As the documentation says "This function is a variation on the usual multdimensional scaling (or principle coordinate) plot". Statisticians are sometimes not very imaginative when choosing names for things, but PCA is an abbreviation for "principle component analysis" which is not the same as "principle coordinate analysis". Best wishes Gordon > Date: Tue, 21 May 2013 11:55:36 -0700 (PDT) > To: "Bioconductor@r-project.org" <bioconductor@r-project.org> > Subject: [BioC] edgeR MDS > > Hello, > > I am working on edgeR version 3.2.3. > >> From the documentation, I guess the "plotMDS.DGEList" is similar to >> PCA. The manual mentions that "Distances on the plot represent >> coefficient of variation of expression between samples". > > Is it possible to get a value of proportion of variance explained from > each dimension (component)? Also, is it possible to use the DGEList to > make a 3D PCA plot? > > Thanks, > > Manoj. > > > Manoj Hariharan > Staff Researcher > The Salk Institute for Biological Studies > La Jolla, CA 92037 > Office: 858.453.4100 x2143 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:8}}