The VSN proposed by , which generalises a VST method proposed in , is notorious for assuming that the various libraries in the dataset can be treated as technical replicates; i.e, most genes are not differentially expressed between conditions. When analysing a cell differentiation time-course, this is hardly an acceptable assumption.
With regards to the VST method implemented in DESeq, I am trying to figure out if it relies on the same assumption as above. While it is well established that there are undesirable artefacts introduced when the sequencing depths of each library are wildly different, I was not able to find a literature reference with regards to the type of limitation described above. However, a forum post by Huber appears to suggest that the limitation does indeed exist .
Could someone please confirm or deny whether the VST method implemented in DESeq assumes that the samples can be treated as technical replicates?
 Huber et al, 2002
 Durbin et. al, 2002