Often, high-ranking DTU hits are just gene switch on/off events, where the very few transcripts seen in one of the two conditions can create an artificially massive change in isoform proportions.
Set better noise criteria, or find a way to flag and discount gene on/off events and marginal above-noise cases.
It is not RATs' intention to identify significant DGE in general, but when one of the conditions is very lowly expressed, it leads to results I do not find particularly convincing.
Often, high-ranking DTU hits are just gene switch on/off events, where the very few transcripts seen in one of the two conditions can create an artificially massive change in isoform proportions.
Set better noise criteria, or find a way to flag and discount gene on/off events and marginal above-noise cases. It is not RATs' intention to identify significant DGE in general, but when one of the conditions is very lowly expressed, it leads to results I do not find particularly convincing.