Table 1.

Mean (SD) number of positive SNPs at significance level α and fraction of samples f in stage one and for sample sizes 100, 200, and 300 for each method (one-stage design, two-stage design, and two-stage design with clustering)

		100			200			300
α	f	1 stage	2 stage	2 stage-c	1 stage	2 stage	2 stage-c	1 stage	2 stage	2 stage-c
0.05	0.3		15.8(± 0.42)	6.8(± 0.20)		27.6(± 0.54)	10.7(± 0.25)		39.7(± 0.62)	15.0(± 0.29)
	0.4	17.9(± 0.44)	16.1(± 0.43)	6.5(± 0.19)	31.1(± 0.62)	28.3(± 0.58)	11.3(± 0.25)	44.9(± 0.71)	40.1(± 0.63)	15.3(± 0.27)
	0.5		16.1(± 0.42)	6.9(± 0.18)		28.2(± 0.56)	11.4(± 0.26)		40.5(± 0.64)	15.7(± 0.27)
0.01	0.3		14.0(± 0.41)	6.0(± 0.20)		24.6(± 0.48)	9.8(± 0.23)		35.6(± 0.57)	13.5(± 0.27)
	0.4	15.7(± 0.41)	14.2(± 0.38)	6.0(± 0.18)	27.6(± 0.54)	25.0(± 0.47)	10.4(± 0.22)	39.4(± 0.62)	36.0(± 0.54)	14.0(± 0.26)
	0.5		14.2(± 0.39)	6.2(± 0.16)		25.1(± 0.48)	10.3(± 0.23)		36.1(± 0.56)	14.3(± 0.25)