The P-values with lfcShrink and ashr shrinkage estimator
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haasroni • 0
@haasroni-20191
Last seen 6 days ago
United States

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!

DESeq2 • 153 views
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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

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

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

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