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).

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

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

• More information on results columns (see third point under 'Note on p-values set to NA')

Kevin