Why s-values instead of p-values with non-default lfcThreshold and apeglm shrinkage in DESeq2
1
0
Entering edit mode
@jabaronphd-23738
Last seen 4.5 years ago

Why does setting lfcThreshold > 0 in lfcShrink() of DESeq2 report s-values instead of p-values when using apeglm shrinkage?

Currently using Bioconductor 3.10, DESeq2 1.26.0

deseq2 apeglm • 1.0k views
ADD COMMENT
1
Entering edit mode
@mikelove
Last seen 1 day ago
United States

The p-values are from a null hypothesis test produced by results, but lfcShrink can also produce s-values, and it can test against an LFC threshold. It is just confusing If you want threshold test p-values and posterior estimates of LFC together in the same table, I'd just make two tables (one with results and one with lfcShrink) and then add the relevant column from one to the other.

ADD COMMENT

Login before adding your answer.

Traffic: 432 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6