**10**wrote:

This may be a simple question but i don't know how to answer (I'm new in bioinformatics). Briefly, a couple of months ago I did my analysis of differential expression using DESeq2 and my last command line to obtain de differentially expressed genes between my two conditions was: results <- subset(results, padj < 0.05). After all the next data interpretation i wrote my final work and in the section of materials and methods i described it this way: Differential expression analyses were performed using DESeq2 R-package (v.1.22.1) with a P < 0.05 (Love, 2014). But then one of my reviewers asked me why hadn't i considered a cutoff of fold change to get DEG which is typical in this kind of analysis?

I have to mention that in the results of the DESeq2 i have something like this: LFC > 0 (up) : 138, 100% LFC < 0 (down) : 0, 0%

Does that mean that my LFC was =0? Is this value a default parameter? because i never set it.

I honestly have no idea what to answer because after reading the paper of DESeq2 i thought that the padj (or P value) was like setting the fold change cutoff. Can someone explain this to me? or my results are wrong? if the p value is different to the fold change cutoff how can i justify that i used the p value? Thanks in advance.