Hi,

I've had instances in the past of getting p-value or p-adj value as NA, which I've now understood from the forum why. But, recently, while running an LRT design, I received p-value/p-adj value as 0. Since I'd given a significant cut-off as <0.05, this result got picked up.

Would it be advisable to consider this result?

You can get very small p-values when the null hypothesis is trivially false. E.g. here, do the counts have expected value equal to 1?

> dds <- makeExampleDESeqDataSet()
> design(dds) <- ~1
> dds <- DESeq(dds)
> min(results(dds)$pvalue)
[1] 0