I am a bit confused about the rlog() and vsd() functions in DESeq2.
Using log2 transformation, it is quite clear how to proceed for normalisation and then log2 transformation of data. It is however not possible to normalise the data before applying rlog or vst on them. I see from the document that normalisation is done sort of behind the scene in these two cases.
What I see is that the shape of the distribution looks quite different using log2 vs. rlog vs. vsd. In the case of the graph above, it seems if sufficient filtering of raw counts are done, log2 transformation works quite good. I was wondering what is your idea about that and also why rlog values start from below zero?