Table 2.

Summary of comparisons.

	Library size				Input subtraction
	Effective	Full	TMM	MAnorm	None	scale CPM
edgeR default	x		x		x
edgeR full		x			x
DiffBind default	x		x			x
DiffBind full		x	x			x
MAnorm3	x*			x	x
Voom		x			x

Each type of analysis is shown with a different row with X indicating the option(s) that was chosen.

^*MAnorm3 takes the average of log transformed effective library sizes for scaling.