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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 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!

The s-value for

`ashr`

is only added if you set`svalue=TRUE`

, so set it to FALSE if you want the p-values.See: https://github.com/mikelove/DESeq2/blob/master/R/lfcShrink.R#L479-L487

Thanks! But what if I want the s-values and also the P-values that were used to calculate the s-values?

`svalue`

are not calculated from p-values. See the Stephens 2016 paper and also the apeglm paper for details.