Table 3.

Type I error of score tests, as a function of haplotype diversity

		Haplotype analyses			Cluster analyses
Diversity	Haplotypesa	α = 0.05	α = 0.01	d.f.b	α = 0.05	α = 0.01	d.f.b
6 Markers
Low	4.2	0.031	0.001	3.17	0.060	0.012	1.21
Medium	10	0.022	0.003	8.70	0.035	0.003	4.02
High	17	0.015	0.001	15.40	0.035	0.002	7.12
Very high	28	0.010	0.002	23.02	0.040	0.007	10.06
8 Markers
Low	5.2	0.027	0.006	4.18	0.042	0.007	1.00
Medium	15	0.030	0.003	11.53	0.047	0.010	4.81
High	25	0.011	0.000	21.28	0.038	0.005	8.82
Very high	48	0.002	0.000	40.15	0.025	0.001	23.18

^aMean haplotype diversity over samples of 200 each RA cases and controls taken from 50 different Problem 3 replicates.

^bDegrees of freedom from the score test averaged over 1000 samples of 150 each cases and controls analyzed with adjustment for sex and DRB1*04 alleles.