Hi Dears, I may take your few minutes?

After DESeq2 analysis, I found pretty small number of significant genes with a cut of point padj < 0.05. When I try with padj < 0.1, it become two much. I wonder if I can use non-adjusted p value with a lower cutoff point (p-value < 0.01) or is there any way to correct it?

Best; Amare

Hi, this is a question unrelated to the DESeq2 package. If you would like advice on which filter for statistical significance to use, then I would try a more general forum for bioinformatics or statistics.

In my own opinion based on experience, you will struggle to publish your work if you use nominal / un-adjusted p-values because it immediately leaves more room for error in your results. It would probably be better to go by 10% FDR (padj < 0.1); however, even doing this will still make it more difficult for you to publish your work.

Kevin