Question: How are Count values normalized in DEseq2?
0
gravatar for john.perish
12 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 • 912 views
ADD COMMENTlink modified 12 months ago by swbarnes24.5k • written 12 months ago by john.perish0
0
gravatar for Carlo Yague
12 months ago by
Carlo Yague4.3k
Belgium
Carlo Yague4.3k 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 12 months ago by Carlo Yague4.3k
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gravatar for swbarnes2
12 months ago by
swbarnes24.5k
United States
swbarnes24.5k 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 12 months ago by swbarnes24.5k
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