Dispersion shrinkage in DESeq2: LOESS instead of negative binomial based GLM?
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chenggyan • 0
@chenggyan-21848
Last seen 4.6 years ago

DESeq2 uses GLM with negative binomial distibution to shrink variance. It seems that GLM is used because the expression variance is different for gene with different expression level and a ordinary linear model is not suited. I am wonder if it is possible to model this regressor using LOESS instead of GLM?

deseq2 RNA-Seq • 398 views
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@mikelove
Last seen 5 hours ago
United States

Take a look at the DESeq2 paper from 2014. A couple of parts to the method are being conflated in your question.

Also see the vignette on the “local” dispersion estimation.

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