Inquiry about deseq2 transformation

Question

[Chen]

Hi everyone, I have a question about the deseq2 transformation and really appreciate your answers.

There is one sentence in deseq2 tutorial: ' The point of these two transformations, the VST and the rlog, is to remove the dependence of the variance on the mean, particularly the high variance of the logarithm of count data when the mean is low.' I was wondering how to interpret the meaning of mean because I thought transformation was used to remove the effect of both sequencing depth and gene length. Thank you in advance :).

Answer 1

[ATpoint]

The transformations first correct for sequencing depth (and composition) and then apply the variance stabilization / regularization. No correction for length is applied. Does this answer the question?

[Chen]

that's helpful, thanks :)