Hello,

I am using Diffbind to find differentially enriched peaks between healthy and disease groups. After creating the dba_object using dba() and filtering the blacklist and graylist regions with dba.blacklist(), I proceeded with dba.count(..., score=DBA_SCORE_NORMALIZED) to generate the binding matrix. From my understanding, setting score=DBA_SCORE_NORMALIZED uses normalized read counts instead of raw counts.

In this case, do I still need to explicitly run dba.normalize() next before proceeding with further steps, such as dba.contrast() and dba.analyze()?

I am a bit confused about the normalization performed by dba.count versus dba.normalize. Could someone kindly clarify the differences and their respective roles?

Thank you very much for your help!