DESEQ2: Some genes have empty pvalue and padj
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Bine ▴ 10
@bine-23912
Last seen 5 weeks ago

Dear all,

Has anyone an idea why some of my results from a DESEQ2 analysis have empty pvalue and padj value. Most of the genes have a pvalue and padj but for some genes for a reason I dont understand they are completely empty. In case the value is 0 for other genes it would show a "0". So empty seems not to be equal to zero.

Example:

log2FoldChange pvalue padj
2
2
1 2.03843E-05 0.023951556
1 0.00070128 0

Line 1 and 2 have no pvalue and no padj.

Thank you for any ideas!

Bine

DESeq2 • 112 views
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@mikelove
Last seen 13 hours ago
United States

This is not because of DESeq2 code. results always outputs a number or NA.

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Okay thanks for clarifying. Actually I just realized that it shows NA in R but then when printing to Excel it gets empty. This I can fix.

But still dont understand then why some values it has NA ?

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Read the manual, unsurprisingly it is covered there: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-are-some-p-values-set-to-na

It is very unlikely that you will stumble over an issue that cannot be solved by reading the manual, or browsing this community (e.g. via google where it is indexed or the in-built search function), or searching biostars.org for it. Most (if not all) standard issues have been asked before given the heavy use of DESeq2 across the bioinformatics community. Please put in some effort.

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