Combining multiple hypothesis testing and affinity propagation clustering leads to accurate, robust and sample size independent classification on gene expression data

Sakellariou, Argiris; Sanoudou, Despina; Spyrou, George

doi:10.1186/1471-2105-13-270

Table 3 The FS methods sorted by the AUC metric achieved in validation test for each cancer disease using the RF classifier

From: Combining multiple hypothesis testing and affinity propagation clustering leads to accurate, robust and sample size independent classification on gene expression data

	FS methods	5-CV			Hold-out Validation
		AUC	TNR	TPR	AUC	TNR	TPR
BREAST	m AP -KL	0.80 (0.11)	0.79 (0.16)	0.73 (0.18)	0.87	1.00	0.50
	maxT(200)	0.85 (0.11)	0.83 (0.13)	0.69 (0.17)	0.83	0.71	0.83
	PLS-CV	0.91 (0.08)	0.85 (0.13)	0.77 (0.15)	0.82	0.86	0.42
	RF-MDA	0.91 (0.07)	0.91 (0.11)	0.70 (0.16)	0.82	0.86	0.75
	maxT	0.87 (0.10)	0.84 (0.13)	0.74 (0.18)	0.77	0.71	0.58
	SAM	0.82 (0.11)	0.79 (0.15)	0.69 (0.19)	0.77	0.71	0.75
	SNR	0.86 (0.10)	0.85 (0.14)	0.72 (0.20)	0.77	0.71	0.67
	BGA-COA	0.83 (0.10)	0.79 (0.15)	0.67 (0.15)	0.76	0.57	0.58
	HykGene	0.91 (0.06)	0.86 (0.12)	0.76 (0.17)	0.76	0.71	0.75
	Rnd	0.79 (0.01)	0.76 (0.03)	0.65 (0.03)	0.76	0.70	0.78
	cat	0.91 (0.07)	0.86 (0.12)	0.78 (0.16)	0.75	0.71	0.50
	PCA	0.72 (0.14)	0.66 (0.18)	0.56 (0.19)	0.75	0.43	0.67
	ODP	0.83 (0.10)	0.80 (0.14)	0.69 (0.18)	0.74	0.71	0.58
	t-test	0.82 (0.10)	0.81 (0.14)	0.69 (0.19)	0.73	0.71	0.58
	eBayes	-	-	-	-	-	-
COLON	m AP -KL	0.99 (0.03)	0.95 (0.12)	0.97 (0.09)	0.89	0.71	0.84
	BGA-COA	0.98 (0.06)	0.89 (0.22)	0.87 (0.19)	0.87	0.71	0.80
	Rnd	0.98 (0.02)	0.90 (0.06)	0.90 (0.03)	0.84	0.73	0.82
	maxT(200)	1.00 (0.00)	0.94 (0.13)	0.94 (0.13)	0.83	0.71	0.88
	PCA	0.79 (0.19)	0.80 (0.23)	0.72 (0.26)	0.83	0.43	0.84
	ODP	0.99 (0.03)	0.97 (0.13)	0.93 (0.13)	0.82	0.71	0.80
	HykGene	0.98 (0.06)	0.93 (0.14)	0.95 (0.12)	0.81	0.71	0.88
	RF-MDA	0.99 (0.03)	0.96 (0.11)	0.93 (0.13)	0.81	0.71	0.80
	eBayes	0.99 (0.03)	0.97 (0.11)	0.93 (0.13)	0.80	0.71	0.80
	SAM	1.00 (0.02)	0.99 (0.09)	0.93 (0.13)	0.80	0.71	0.80
	cat	0.99 (0.04)	0.97 (0.14)	0.93 (0.13)	0.80	0.57	0.80
	maxT	1.00 (0.02)	0.97 (0.10)	0.94 (0.13)	0.79	0.71	0.80
	PLS-CV	1.00 (0.02)	0.94 (0.16)	0.94 (0.13)	0.79	0.71	0.80
	SNR	0.99 (0.03)	1.00 (0.00)	0.93 (0.13)	0.79	0.71	0.80
	t-test	0.99 (0.03)	0.99 (0.05)	0.93 (0.13)	0.79	0.71	0.80
LEUKEMIA	BGA-COA	0.99 (0.04)	1.00 (0.00)	0.81 (0.27)	1.00	1.00	0.86
	maxT(200)	1.00 (0.00)	1.00 (0.00)	1.00 (0.00)	1.00	1.00	0.86
	eBayes	1.00 (0.00)	1.00 (0.00)	0.91 (0.19)	1.00	0.95	0.93
	RF-MDA	1.00 (0.00)	1.00 (0.00)	1.00 (0.00)	0.99	1.00	0.86
	PLS-CV	1.00 (0.00)	1.00 (0.00)	0.89 (0.25)	0.99	0.95	0.93
	SAM	1.00 (0.00)	1.00 (0.00)	0.91 (0.19)	0.99	0.95	0.93
	cat	1.00 (0.00)	1.00 (0.00)	0.95 (0.14)	0.99	0.95	0.93
	HykGene	1.00 (0.00)	1.00 (0.00)	0.90 (0.20)	0.97	0.90	0.93
	Rnd	0.99 (0.01)	0.98 (0.02)	0.86 (0.06)	0.97	0.99	0.75
	maxT	1.00 (0.02)	0.98 (0.07)	0.85 (0.27)	0.96	1.00	0.64
	mAP-KL	1.00 (0.00)	1.00 (0.00)	0.97 (0.17)	0.71	0.90	0.43
	PCA	0.56 (0.16)	1.00 (0.00)	0.00 (0.00)	0.64	0.95	0.14
	SNR	0.50 (0.00)	1.00 (0.00)	0.00 (0.00)	0.50	1.00	0.00
	t-test	0.50 (0.00)	1.00 (0.00)	0.00 (0.00)	0.50	1.00	0.00
	ODP	-	-	-	-	-	-
PROSTATE	SAM	0.96 (0.04)	0.97 (0.05)	0.88 (0.10)	0.92	0.00	1.00
	maxT(200)	0.95 (0.10)	0.95 (0.10)	0.89 (0.10)	0.88	0.00	1.00
	PLS-CV	0.97 (0.03)	0.95 (0.08)	0.92 (0.07)	0.87	0.33	1.00
	eBayes	0.96 (0.04)	0.98 (0.04)	0.89 (0.10)	0.86	0.00	1.00
	RF-MDA	0.97 (0.04)	0.97 (0.06)	0.90 (0.09)	0.83	0.11	1.00
	mAP-KL	0.93 (0.06)	0.90 (0.09)	0.85 (0.11)	0.80	1.00	0.36
	BGA-COA	0.95 (0.05)	0.91 (0.09)	0.89 (0.10)	0.73	0.22	0.88
	Rnd	0.93 (0.02)	0.89 (0.04)	0.86 (0.03)	0.70	0.18	0.94
	HykGene	1.00 (0.00)	1.00 (0.00)	1.00 (0.00)	0.69	0.89	0.24
	maxT	0.89 (0.07)	0.88 (0.09)	0.79 (0.13)	0.50	0.00	1.00
	PCA	0.84 (0.09)	0.77 (0.15)	0.75 (0.15)	0.50	0.00	1.00
	SNR	0.50 (0.00)	0.08 (0.27)	0.92 (0.27)	0.50	0.00	1.00
	t-test	0.50 (0.00)	0.08 (0.27)	0.92 (0.27)	0.50	0.00	1.00
	ODP	-	-	-	-	-	-
	cat	-	-	-	-	-	-

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ISSN: 1471-2105

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