I was wondering how Diffbind deals with the problem of using multiple blocking factors (let's say, age, gender and postmortem delay). If there is a (small) limit of how many of those I could correct at the same time. Ideally, two or three should be possible (for example, those three I named, in sequencing data from tissue, are very important and almost always are playing a role in the biological interpretation).

The cases I have seen in the tutorial are for when you only have one blocking factor. In the case that I have data for two or three variables at the same time, what's the best way of doing it? Should I correct this manually myself somehow, or Diffbind provides a way? Thank you very much for your time.

The upcoming release of DiffBind will support the ability to include arbitrary designs and complex contrasts, made up of any of the metadata factors Tissue, Factor, Condition, Treatment, Replicate, and Caller. So one could for example have a design such as:

design = "~Replicate + Treatment + Tissue + Condition"

and set any of the design matrix coefficients however you like for testing, e.g.

contrast = c("Condition","Disease","Control")