Table 1.

Methods and parameter configurations compared in this paper

Key	Software	Configuration parameters
DESeqPgO	DESEq	method=~pooled~, sharingMode=~per-condition~
DESeqPmax	DESEq	method=~pooled~, sharingMode=~maximum~
DESeqCgO	DESEq	method=~per-condition~, sharingMode=~per-condition~
DESeqCmax	DESEq	method=~per-condition~, sharingMode=~maximum~
edgeRdf20	edgeR	common/trended/tagwise moderation regime with prior.df=20 (default)
edgeRdf1	edgeR	common/trended/tagwise moderation regime with prior.df=1
edgeRqlfDf20	edgeR	common/trended/tagwise moderation regime with prior.df=20 (default) and quasi-likelihood F-tests
edgeRqlfDf1	edgeR	common/trended/tagwise moderation regime with prior.df=1 and quasi-likelihood F-tests