p adjusted value not available
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marie • 0
@marie-19926
Last seen 9 days ago

Hi, I am running ‘DESeq2’ version 1.28.1. Sometimes padj is not available when p-value is available. Could somebody tell me how it happens and how to set the threshold? (I used to use padj < 0.05).

<h3>#</h3>

baseMean log2FoldChange lfcSE stat pvalue padj

gene1 1095.443243 0.435315299 0.088444843 4.921884483 8.57E-07 0.00521146

gene2 165.3255191 0.6522744 0.143368231 4.54964391 5.37E-06 NA

gene3 255.7587247 -0.899313382 0.200596466 -4.483196551 7.35E-06 NA

gene4 835.7429698 0.478818072 0.115020125 4.162906915 3.14E-05 0.095523332

gene5 2028.101825 0.251523233 0.064565536 3.895626804 9.79E-05 0.097713818

StatisticalMethod DESeq2 • 43 views
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I think I found a similar past question. So, I'd like to resolve this issue.

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@u16406
Last seen 4 hours ago
Republic of Ireland

Indeed, marie, the answer can be found in the DESeq2 vignette:

Kevin

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