The descriptions of score methods in DiffBind manual are trimmed and cannot be understood in its pdf file (fig1). Could you provide them for me to learn? Many thanks. By the way, the default is DBA_SCORE_TMM_MINUS_FULL?
You are correct about the default score, however this is only used for plots, and only when the entire experiment if plotted. When data form a speicic contrast is used, the normalised counts from that comparison are plotted and/or reported.