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

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