The P-values with lfcShrink and ashr shrinkage estimator

Question

[haasroni]

Hi all,

As I understand, s-values are calculated if using the lfcShrink function (with svalue = TRUE), instead of p-adjusted values in results. Is there a way I can get the nominal P-values (used to calculate the s- values) and also the s-values, by using the ashr shrinkage estimator? I only see the s-values.

If not, which P-values is it base on? How can I examine my test by P-value histogram and volcano plots for example?

Thank you!

Answer 1

[ATpoint]

Answered by the DESeq2 developer: https://support.bioconductor.org/p/9138276/#9138347