Table 2.

Simulation study

								Mean Square Error (×103)
I	π	eβ	σ	SIM	NAIVE	THRES	LC	NAIVE	THRES	LC
50	0.8	1.3	(0.15,0.15)	1.23	1.17	1.15	1.20	57	87	42
50	0.8	1.3	(0.2,0.2)	1.24	1.14	1.09	1.21	107	131	114
50	0.8	1.3	(0.15,0.2)	1.28	1.18	1.15	1.24	134	148	112
50	0.8	2	(0.15,0.15)	1.60	1.40	1.28	1.48	54	85	44
50	0.8	2	(0.2,0.2)	1.82	1.36	1.29	1.52	152	158	126
50	0.8	2	(0.15,0.2)	1.89	1.42	1.33	1.57	180	253	162
50	0.5	1.3	(0.15,0.15)	1.26	1.24	1.21	1.26	39	51	32
50	0.5	1.3	(0.2,0.2)	1.32	1.28	1.25	1.35	82	79	97
50	0.5	1.3	(0.15,0.2)	1.26	1.23	1.20	1.26	66	72	60
50	0.5	2	(0.15,0.15)	2.04	1.94	1.83	2.05	40	67	34
50	0.5	2	(0.2,0.2)	2.04	1.76	1.68	2.05	107	128	92
50	0.5	2	(0.15,0.2)	2.06	1.78	1.72	1.99	87	107	71
300	0.8	1.3	(0.15,0.15)	1.30	1.25	1.18	1.30	13	32	10
300	0.8	1.3	(0.2,0.2)	1.32	1.25	1.15	1.34	27	50	29
300	0.8	1.3	(0.15,0.2)	1.30	1.22	1.16	1.29	24	42	21
300	0.8	2	(0.15,0.15)	2.01	1.87	1.49	2.01	21	120	13
300	0.8	2	(0.2,0.2)	2.03	1.70	1.36	1.99	69	203	43
300	0.8	2	(0.15,0.2)	2.03	1.62	1.38	1.86	78	189	38
300	0.5	1.3	(0.15,0.15)	1.31	1.27	1.26	1.30	7	9	5
300	0.5	1.3	(0.2,0.2)	1.30	1.23	1.22	1.30	15	17	12
300	0.5	1.3	(0.15,0.2)	1.30	1.24	1.23	1.29	12	14	9
300	0.5	2	(0.15,0.15)	2.00	1.87	1.77	2.00	11	23	5
300	0.5	2	(0.2,0.2)	2.00	1.72	1.66	2.02	36	51	15
300	0.5	2	(0.15,0.2)	2.00	1.76	1.71	1.97	26	37	10

Odds ratio (e^β) and mean square error obtained in 1,000 simulations using the three different approaches, NAIVE, THRES and LC (see text for a description of each). Results are given for different scenarios, varying the number of individuals (I), the proportion of individuals with each copy number status (π), the odds ratio (e^β), and the variance for CNV quantitative measurements.