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[BUG] padj=nan when pvalue is not nan #355

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ggg5438 opened this issue Jan 10, 2025 · 1 comment
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[BUG] padj=nan when pvalue is not nan #355

ggg5438 opened this issue Jan 10, 2025 · 1 comment
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@ggg5438
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ggg5438 commented Jan 10, 2025 •
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Hello,
Thank you for your package. It helps me a lot. (especially I don"t want to use R)

I found that some padj values are nan when corresponding p-values are not nan.
Among 12,308 genes, 1,223 padj values are nan, even though all foldchange values are not nan and only 43 raw p-values are nan.

I have two questions:

  1. Why some raw p-values have nan values even when their fc and stat values are not nan?
  2. Why padj values have nan values when raw p-values are not nan?
@ggg5438 ggg5438 added the bug Something isn't working label Jan 10, 2025
@BorisMuzellec
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Hi @ggg5438, thank you for your interest in our package.

This is not a bug.

  1. Unadjusted. p-values may be set to nan when a gene contains an extreme outlier value. The adjusted p-value for this gene will be in turn set to nan. This can be controlled by setting cooks_filter to True or False in DeseqStats.
  2. A padj may be set to nan even though its unadjusted counterpart is not nan due to independent filtering (independent_filter in in DeseqStats).

See also the DESeq2 vignette on this topic.

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@ggg5438 @BorisMuzellec