I've got a chip-seq dataset which I would like to analyse using DiffBind. I've tried Diffbind with one blocking factor and it works fine, but I was wondering how can I do it for three factors (e.g. age, gender, post-mortem delay , when dealing with tissue samples). (E.g. sample 1 : 60 years old, female , 24 hours. ) I ask how to do it because it seems I have to put one of my variables as the "Factor" column in the SampleSheet for the program to easily recognize it as a blocking factor, but not any column will do (e.g. if I make three columns named Age, Gender and PMD, the program does not make the model with them).

Any ideas of what to do in such case? 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")