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irish.prg • 0
@9ba0e448
Last seen 5 weeks ago
Indonesia

Hi all. I want to ask something about DESeq2 statistics. I've got the my DESeq2 results but there are so many datas with pvalue > 0.05, so it means the differential gene expression is not significant.

There are also datas that have NA in its Padj. The question I want to ask is, if the Padj is NA because either the controlmean/experimentalmean are 0, can I use pvalue instead to measure the significancy of the differential gene expression?

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@mikelove
Last seen 4 hours ago
United States

See the vignette which describes why the padj can be NA, while the pvalue is not. See independentFiltering argument of ?results.

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Yes, but my question was if the padj result is NA, is it okay if i use pvalue for the statistic?

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In short, no these are not appropriate to consider, see the workflow for more discussion on why not.