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

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