Question: How are Count values normalized in DEseq2?
0
gravatar for john.perish
2.3 years 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 • 1.7k views
ADD COMMENTlink modified 2.3 years ago by swbarnes27.6k • written 2.3 years ago by john.perish0
0
gravatar for Carlo Yague
2.3 years ago by
Carlo Yague5.0k
Canada
Carlo Yague5.0k 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 2.3 years ago by Carlo Yague5.0k
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gravatar for swbarnes2
2.3 years ago by
swbarnes27.6k
United States
swbarnes27.6k 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 2.3 years ago by swbarnes27.6k
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