Both of the tools use different kind of data transformation for doing PCA plots.
However, in the the comparison the plots look quite different, the sample get separated in a different manner. And I have now the same problem.
The MDS plot from edgeR shows almost what I expect (batch effect between the samples) but DESeq PCA plot is different, not showing the expected batch effect.
Why is there such a difference and can different transformations of the data effect the PCA that much?