Update. 11/13/17 Thanks to Mike Love for pointing out an error. This is just my understanding. There maybe other errors.
To allow complex study designs in iDEP(http://ge-lab.org/idep/
), I tried to understand how factoral models are built and the desired results are extracted from DESeq2. The following is based on the help document from the resutls( ) function in DESeq2, plus some of Mike Love’s answers to questions from users.