Table 4.

Accuracy comparison of three methods for various CNV sizes. All accuracy indexes are listed as percentages. The average tuning parameters used in the fused lasso were λ₁ =0.13 (0.04) and λ₂ = 0.77 (0.22); standard deviations appear in parentheses. For DPI, the 3-fold cross-validation accuracy indexes are averages over the leftover thirds; initial values of average LogR for each copy number state: μ₀ = −5.5923, μ₁ = −0.6313, μ₂ = −0.0045, μ₃ = 0.3252

		PennCNV			Fused Lasso			DPI
CNV size	CNV type	TPR	FPR	FDR	TPR	FPR	FDR	TPR	FPR	FDR
5	Del	83.80	0.0017	4.92	76.67	0.0202	40.66	76.67	0.0006	1.88
	Dup	58.53	0.0011	4.67	00.33	0.0065	98.05	53.60	0.0003	1.28
10	Del	95.03	0.0011	1.45	94.23	0.0130	15.21	89.37	0.0005	0.77
	Dup	93.43	0.0006	0.78	26.00	0.0128	39.01	92.30	0.0006	0.89
20	Del	94.63	0.0008	0.58	96.97	0.0159	09.62	89.87	0.0016	1.15
	Dup	96.13	0.0014	0.92	74.93	0.0126	09.86	95.50	0.0011	0.76
30	Del	94.57	0.00130.62	0.28	96.76	0.0156	06.53	94.73	0.0013	0.62
	Dup	96.09	0.0001	0.05	85.84	0.0173	08.02	95.39	0.0012	0.55
40	Del	97.83	0.0018	0.59	98.33	0.0158	04.94	98.46	0.0006	0.19
	Dup	94.61	0.0014	0.46	87.88	0.0181	06.24	94.66	0.42	0.42
50	Del	94.33	0.0003	0.07	95.49	0.0162	04.21	93.82	0.0010	0.26
	Dup	94.50	0.0003	0.09	91.06	0.0121	03.33	95.03	0.0011	0.30
Overall		94.42	0.0009	0.49	88.00	0.0147	07.73	93.70	0.0009	0.50