Apparent "wings" in volcano plots (for example, as seen here) are evidence for the relationship between fold change and p-value when expression is low in one condition and there are few replicates. If one wishes to remove or minimize these, that can be done by pre-filtering the counts matrix (for example, excluding rows with partial or complete row sums/means/etc. below some user-defined threshold) and/or performing shrinkage for the effect size estimates.
My main question is this: Is it a problem/mistake to not remove or otherwise minimize "wings"?
- If it is necessary to address these "wings", is it suitable to do shrinkage without counts-matrix filtering or vice versa?
- Any advice on setting thresholds for counts-matrix filtering in a non-arbitrary way?