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@udel.edu Ph: 832-566-0011 [[alternative HTML version deleted]]