DESeq2 - shrunken log fold changes and threshold test
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@corentinrichard374369-18463
Last seen 2.7 years ago

Hello everyone,

 

I have just read the vignette about DESeq2 and I have a question about shrunken log fold changes and threshold test.

I use DESeq() and results() functions to get the gene set with absolute LFC > 1. I understood that the tests give me the results with LFC estimated by MLE.

However, some absolute LFC become lower than 1 after being shrunk by lfcShrunk function.

 

Is it possible and does it make sense testing for statistical significance of absolute LFC > 1 estimated by MAP (apeglm) ?

 

I apologize if the question has been asked before.

Thanks in advance,

 

Corentin

deseq2 lfcshrink lfcthreshold differential gene expression • 355 views
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@mikelove
Last seen 4 days ago
United States

We do have inference for the posterior (shrunken) LFC but instead of the point null, we estimate posterior probability of false sign and use the s-value as defined by Stephens. It is analogous to the q-value or adjusted p-value but for bounding the rate of false sign. Just set svalue=TRUE. There is some more explanation in the DESeq2 and the apeglm vignettes.

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