Dear Sridhara, Not exactly. Dimension 1 is the direction that best separates the samples, without regard to whether they are treatments or replicates. Dimension 2 is the next best direction, uncorrelated with the first, that separates the samples. It may turn out that one dimension separates treatments and one separates batches, but this depends entirely on your data. For more information about MDS plots, try ?cmdscale. Best wishes Gordon > Date: Thu, 31 Mar 2011 10:07:28 -0400 > From: Sridhara Gupta Kunjeti <sridhara at="" udel.edu=""> > To: bioconductor at r-project.org, bioconductor-request at r-project.org > Subject: [BioC] edgeR - MDS plot > > Hello, > I am new to this kind of analysis in MDS plot. I used edgeR for DGE > analysis, which showed a great analysis of my results. I have one specific > question regarding the MDS plot. > For example, for my data sets: > F0a, F0b > P3a, P3b > P6a, P6b > where a and b are replicates. > > when I plot them on MDS, what does the dimension1 and dimension2 mean in the > MDS plot (and what is the units on x and y-axis). If I understand correctly, > Dimension 1 is the variation (tell how different are the replicates -- eg., > F0a and F0b) and Dimension 2 tells how different are the treatments (eg., > F0's with P3's). Please correct me if I am wrong. > > Any suggestions will he highly appreciated. > > Many thanks! > Sridhara > > > -- > Sridhara G Kunjeti > PhD Candidate > University of Delaware > Department of Plant and Soil Science > email- sridhara at udel.edu > Ph: 832-566-0011 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}