What does one-sided p-value in DESeq2 mean in biological terms?
1
0
Entering edit mode
nash12 • 0
@b501e59c
Last seen 18 days ago
United Kingdom

Dear All,

I am trying to understand what does one tailed p-values calculated in a DESeq2 analysis by setting the lfcThreshold to 0 and specifying the alternative hypothesis (as specified here: post) mean in biological terms. In a standard DESeq2 analysis we test for whether a gene is differentially expressed (DE) or not and a two-sided testing is done. Does the one-sided testing mean that we test whether a gene is DE and is up-regulated or DE and is down-regulated depending on the specification of the alternative hypothesis? Is my understanding correct or am I missing something here?

Also, in case I have multiple RNA-seq studies and I want to do a meta-analysis, can the one-sided p-value obtained from DESeq2 for a gene in each of the studies be used for combination of p-values using the Fisher or Stouffer's method? As is the case in microarray data where one can use one-sided p-values from individual studies for a gene. Or do I need to discard the genes with inconsistent expression direction across studies in case of RNA-seq meta-analysis for DE?

Thank you.

one-sided nbinomWaldTest p-value meta-analysis DESeq2 • 71 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 23 hours ago
United States

To Q1, yes.

What you do with the p-values from DESeq2 is really up to you. Here I focus on software questions.

ADD COMMENT

Login before adding your answer.

Traffic: 139 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