Hello,

Many publications use a combination of both padj and fold change ratio to define differentially expressed genes (DEGs) identified by DESeq2. Would it be valid to submit a manuscript where the DEGs are identified only with a padj threshold?

Many thanks for the opinion on this!

Yes it’s perfectly valid to just use padj. This is what the majority of publications citing DESeq2 do I would say. The choice of whether to use an effect size threshold depends on the system and question.