Question

p value is 0, padj is 0

0

Entering edit mode

Wirayatida • 0

@6677b6ad

Last seen 12 hours ago

Japan

I run DESeq2 in R program. However, I got p-value is 0 and padj is 0. I already remove NA data. How can I solve this problem? Do I need to re-calculate the count from the raw data or not?

DESeq2 • 59 views

ADD COMMENT • link updated 2 hours ago by Michael Love 43k • written 12 hours ago by Wirayatida • 0

score 0 · Answer 1 · 2024-12-12

0

Entering edit mode

James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 3 hours ago

United States

It is quite possible for a very small p-value to remain very small after multiplicity adjustment. I don't know the cutoff for DESeq2 to report a p-value as zero, but apparently that gene has both an adjusted and unadjusted p below that cutoff.

ADD COMMENT • link 5 hours ago James W. MacDonald 67k

0

Entering edit mode

> set.seed(1); t.test(rnorm(200,rep(c(0,80),each=100)) ~ rep(0:1,each=100))$p.value 
[1] 0

ADD REPLY • link 2 hours ago Michael Love 43k