Question: How are Count values normalized in DEseq2?
0
gravatar for john.perish
6 months ago by
john.perish0 wrote:

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

Are these lists normalized in any way?

Thanks!

rna-seq star deseq2 • 431 views
ADD COMMENTlink modified 6 months ago by swbarnes23.6k • written 6 months ago by john.perish0
0
gravatar for Carlo Yague
6 months ago by
Carlo Yague4.0k
Belgium
Carlo Yague4.0k wrote:

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

ADD COMMENTlink written 6 months ago by Carlo Yague4.0k
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gravatar for swbarnes2
6 months ago by
swbarnes23.6k
United States
swbarnes23.6k wrote:

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.

ADD COMMENTlink written 6 months ago by swbarnes23.6k
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