nanoporetech
About RNA methylation difference threshold selection
@ArtRand
When using modkit dmr to identify differential m⁶A modifications—similar to differential expression analysis—is it appropriate to use thresholds such as balanced_effect_size > 0.2 and balanced_map_pvalue < 0.05? Are there any references or recommended guidelines supporting these cutoff values?
Hello @Tang-pro,
Sorry for the terribly long response time (new Modkit features are coming!).
I don't have a specific recommendation regarding the effect size other than making a classical "effect size vs MAP-based p-value" volcano plot. One thing to keep in mind, is if you have very deep coverage, small effect sizes will start to become "significant" and you'll want to use the Cohen's h metric instead. Requiring a balanced_map_pvalue<0.05 is probably an OK place to start, but I haven't looked at this specifically for dRNA runs yet.
