Table 2. Type-1 error using normal cut-off at 0.05 and 0.01 level for 500 trios.

No population stratification,
	Fixed threshold Family-based*					Fixed threshold FBAT-MM*				Fixed threshold Case-control*			No threshold Family-based	No threshold Case-control
	0.005		0.01		0.05	0.005	0.01		0.05	0.005	0.01	0.05
0.05	0.050		0.046		0.046	0.014	0.020		0.030	0.048	0.052	0.054	0.050	0.028
0.01	0.006		0.010		0.010	0.002	0.002		0.002	0.008	0.004	0.010	0.006	0.008
Population stratification, , FST = 0.01
		Fixed threshold Family-based *				Fixed threshold FBAT-MM *				Fixed threshold Case-control *			No threshold Family-based	No threshold Case-control
		0.005	0.01	0.05		0.005		0.01	0.05	0.005	0.01	0.05
0.05		0.048	0.042	0.048		0.018		0.037	0.033	0.260	0.220	0.106	0.048	0.092
0.01		0.014	0.008	0.020		0		0.002	0	0.100	0.086	0.036	0.008	0.034

^*Threshold values 0.005, 0.01 and 0.05 were used for the fixed threshold methods.