The P-values with lfcShrink and ashr shrinkage estimator

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haasroni • 0

@haasroni-20191

Last seen 3.5 years 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 • 1.4k views

ADD COMMENT • link updated 3.6 years ago by Michael Love 43k • written 3.6 years ago by haasroni • 0

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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

ADD REPLY • link 3.6 years ago ATpoint ★ 4.6k

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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?

ADD REPLY • link 3.6 years ago haasroni • 0

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

ADD REPLY • link 3.6 years ago Michael Love 43k

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