Multifactor Analysis in DiffBind

Question

[erbrocato]

Hi,

I have been working with Diffbind to identify differential binding of H3K9me3 due to ethanol treatment. We are using both males and females, and initially ran our male and female groups separately. However, I'm wondering if it's possible to run both sex and treatment as factors. Does anyone know whether the multifactor design is only appropriate to use for normalizing factors such as tissue type or batch? Or could this be used to identify differentially bound regions between two main factors?

Thanks for your help!