There is a problem with this kind of analysis from statistical point of view. (more than two groups)
In practice, DESEq2 use a chisquared like strategy and a binominal test, the analysis is better when you have one vs another group. In the other hand, edgeR is cappable to make this strategy works, but in their own manual this is not advisable and still in test phase, since you can have an "inflation" and false tendency of result. In other words: the logic in RNASeq still working in a 2D universe (difference of AB) and you are talking about 3D (difference of ABC).
In my opinion, you should produce different DGEs crossing the groups (with the same control group if possible) and use a Venn diagram to identify the common findings.
Last edited by luminasapientiae; 03252019 at 09:31 AM.
