Table 1.

Performance of the methods on different tumor types

Tumor	Method	Q2	PPV	TPR	NPV	TNR	C	AUC
COAD	CRank	0.92	0.97	0.86	0.87	0.97	0.84	0.94
	CLow	0.72	0.78	0.66	0.72	0.78	0.47	0.79
	CDiff	0.76	0.78	0.77	0.80	0.74	0.55	0.83
LUAD	CRank	0.97	0.97	0.96	0.96	0.97	0.93	0.99
	CLow	0.84	0.88	0.79	0.81	0.89	0.69	0.91
	CDiff	0.89	0.89	0.90	0.90	0.88	0.79	0.96
PRAD	CRank	0.91	0.92	0.91	0.91	0.92	0.83	0.97
	CLow	0.70	0.66	0.75	0.72	0.74	0.43	0.77
	CDiff	0.79	0.83	0.74	0.77	0.83	0.58	0.87

Note: Performance of ContrastRank, ContrastLow and ContastDiff (respectively, CRank, CLow and CDiff) calculated using an average number 239, 494 and 127 genes with score >3 respectively for COAD, LUAD and PRAD. Q₂, overall accuracy; PPV and NPV, positive and negative predicted values; TPR and TNR, true positive and negative rates; MCC, Matthew’s correlation; AUC = area under the (ROC) curve.