Testing allele homogeneity: the problem of nested hypotheses

Izbicki, Rafael; Fossaluza, Victor; Hounie, Ana Gabriela; Nakano, Eduardo Yoshio; de Bragança Pereira, Carlos Alberto

doi:10.1186/1471-2156-13-103

BMC Genomic Data

Table 6 Analysis of simulated data

From: Testing allele homogeneity: the problem of nested hypotheses

	Genotypes		Alleles			Hardy-Weinberg
						Case		Control
	p ^G	e ^G	$p_{U}^{A}$	p ^A	e ^A	p ^HW	e ^HW	p ^HW	e ^HW
Genotypic Homogeneity
1	0.408	0.773	0.197	0.189	0.786	0.540	0.832	0.819	0.971
2	0.588	0.897	0.648	0.684	0.997	0.030	0.090	0.001	0.002
3	0.478	0.826	0.483	0.510	0.980	0.496	0.793	0.035	0.119
4	0.912	0.996	0.709	0.689	0.997	0.172	0.377	0.122	0.287
5	0.836	0.985	0.578	0.554	0.985	0.224	0.464	0.170	0.378
6	0.989	1.000	0.926	0.903	1.000	0.000	0.000	0.000	0.000
7	0.187	0.494	0.100	0.068	0.498	0.027	0.081	0.044	0.124
8	0.652	0.929	0.444	0.416	0.953	0.338	0.626	0.104	0.257
9	0.620	0.916	0.510	0.494	0.976	0.192	0.422	0.761	0.955
10	0.565	0.888	0.923	0.912	1.000	0.001	0.003	0.057	0.153
Allelic Homogeneity
11	0.008	0.034	0.325	0.291	0.893	0.494	0.790	0.001	0.003
12	0.000	0.000	0.067	0.057	0.442	0.068	0.190	0.000	0.000
13	0.002	0.013	0.151	0.114	0.629	0.989	1.000	0.000	0.000
14	0.001	0.003	0.923	0.918	1.000	0.174	0.400	0.000	0.000
15	0.113	0.342	0.844	0.833	1.000	0.989	1.000	0.006	0.014
16	0.020	0.086	0.559	0.547	0.985	0.174	0.395	0.015	0.040
17	0.001	0.006	0.147	0.129	0.683	0.129	0.319	0.002	0.005
18	0.040	0.149	0.501	0.462	0.970	0.871	0.986	0.001	0.002
19	0.026	0.106	1.000	1.000	1.000	0.760	0.955	0.000	0.000
20	0.001	0.002	0.446	0.379	0.939	0.733	0.938	0.000	0.000
No Homogeneity
21	0.000	0.000	0.925	0.928	1.000	0.000	0.000	0.015	0.045
22	0.843	0.987	0.646	0.618	0.993	0.055	0.153	0.141	0.333
23	0.062	0.219	0.104	0.124	0.661	0.989	1.000	0.007	0.028
24	0.669	0.939	0.403	0.408	0.955	0.994	1.000	0.621	0.882
25	0.000	0.000	0.000	0.000	0.003	0.000	0.000	0.771	0.958
26	0.105	0.331	0.017	0.047	0.403	0.001	0.001	0.001	0.001
27	0.000	0.000	0.000	0.000	0.012	0.072	0.197	0.010	0.033
28	0.180	0.485	0.230	0.233	0.835	0.310	0.598	0.324	0.602
29	0.134	0.387	0.068	0.045	0.389	0.045	0.128	0.063	0.170
30	0.807	0.980	0.522	0.517	0.980	0.806	0.971	0.713	0.933

Results of the simulations under three different scenarios: genotypic homogeneity, allelic (but not genotypic) homogeneity and no homogeneity at all. Bold p values indicate incoherence.

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