Hi,

I was just wondering if anybody knew the adjustment DEP uses for the p.val adj column in it's output?

Thanks

Have you read the help page for test_diff? It says:

Value
       A SummarizedExperiment object containing FDR estimates of differential expression

And FDR is generally assumed to mean Benjamini and Hochberg's method (for example, if you ask p.adjust to use fdr, you get BH).