I have a question about using FDRtool. In the below code (on RNA seq data whose p values were acquired using Deseq2), the FDRtool was first used and thereafter p.adjust using the benjamini hochberg method. Dont they both correct for false discovery rate? Why do you need to run p.adjust after using fdrtool?
FDR.ddsRes <- fdrtool(ddsRes$stat, statistic= "normal", plot = T) ddsRes[,"padj"] <- p.adjust(FDR.ddsRes$pval, method = "BH")