Question

p value is 0, padj is 0

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Wirayatida • 0

@6677b6ad

Last seen 29 days 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 • 481 views

ADD COMMENT • link 4 weeks ago Wirayatida • 0

score 0 · Answer 1 · 2024-12-12

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 2 days 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 4 weeks ago James W. MacDonald 67k

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> 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 4 weeks ago Michael Love 43k

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Thank you so much for your information. I understand it.

ADD REPLY • link 4 weeks ago Wirayatida • 0

score 0 · Answer 2 · 2024-12-12

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swbarnes2 ★ 1.4k

@swbarnes2-14086

Last seen 2 days ago

San Diego

I think the default smallest value R will return is 1x10^-300. So I'd take a look at the counts, and see if it makes sense that the p-values could be that small

ADD COMMENT • link 4 weeks ago swbarnes2 ★ 1.4k

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Than you so much. My counts are 47,37 and 72 for mock. The treatment is 8153, 6723 and 8024.

ADD REPLY • link 4 weeks ago Wirayatida • 0