I following a tutorial from Huber(http://www-huber.embl.de/users/klaus/Teaching/DESeq2Predoc2014.html) for detecting Diff.expressed genes using DESeq2. In the section, 10.2 Inspection and correction of p–values it suggest that if the distribution of raw pvalues follows either hill-shaped histogram or U-shaped hisogram, then the Wald statistic was used re-compute the padj values.
I am working on RNAseq data where I compare the Untreated to knock-down of particular gene. Almost in all my comparisons, I have the hill-shaped the histogram in all my comparison so should I use fdr tool as prescribed in the tutorial to correct my padj values?
When I implement this fdr package my results were drastically changed. Before Fdr package implementation it was 61, after FDR package implementation it came to 260. I am confused now to use which method. Kindly guide me