How are Count values normalized in DEseq2?

Question

[john.perish]

In the output from DEseq2 there are lists of Gene Counts.

Are these lists normalized in any way?

Thanks!

Answer 1

[Carlo Yague]

They can be normalized with the option normalize=T of the function assay(). Usually, if the counts are integer, they are not normalized.

Answer 2

[swbarnes2]

DESeq2 carries out normalization to correct for library size only, based on the premise that most genes are not differentially expressed between all your samples. The procedure is described in the documentation.