This is a question regarding the limma/voom workflow for analyzing RNA-Seq dataset.
According to the workflow described in "RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR", MDS plotting is performed on the DGEList object which was passed through the
calcNormFactors functions. It is performed before executing the
If I understood correctly,
voom is removing heteroscedascity from the count data.
In the DESeq2 vignette ("RNA-seq workﬂow: gene-level exploratory analysis and differential expression") on the other hand, MDS plotting is performed on the
rlog transformed data, which both remove heteroscedascity too. Here it is mentioned that MDS plotting requires removing heteroscedascity.
So for me, right now, it looks like the limma/voom workflow is in contrast to this statement, since
voom - which removes heteroscedascity - is performed after the MDS plotting.
I hope someone can explain why the two workflows seem to differ here.