Table 4. The actual FDR, sensitivity and specificity rate from MAQC2 data given a nominal FDR ≤ 0.05.

Expression quantile cutoff	DESeq			TMM-edgeR			Med-pgQ2			UQ-pgQ2
	Actual FDR	SR	SPR	Actual FDR	SR	SPR	Actual FDR	SR	SPR	Actual FDR	SR	SPR
100%(total)	0.140	0.931	0.609	0.205	0.967	0.358	0.057	0.928	0.854	0.055	0.933	0.861
75%	0.069	0.861	0.806	0.147	0.931	0.516	0.084	0.877	0.758	0.077	0.898	0.774
50%	0.091	0.476	0.926	0.184	0.738	0.740	0.304	0.762	0.482	0.292	0.810	0.482
25%	0.000	0.000	1.000	0.333	0.333	0.917	0.667	0.667	0.333	0.692	0.667	0.250

The sensitivity rate (SR) and specificity rate (SPR) for DEGs analysis by the top methods at the different-quartile cutoffs.