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Table 3 Empirical type-I error estimates in the presence of population substructure

From: Family-based association analysis: a fast and efficient method of multivariate association analysis with multiple variants

     α
TYPE F ST Q D ' 0.005 0.01 0.05
Quantitative 0.01 2 0 0.0048 0.0098 0.0546
2 0.5 0.0066 0.0105 0.0513
5 0 0.0046 0.0098 0.0521
5 0.5 0.0058 0.0105 0.0534
0.05 2 0 0.0054 0.0094 0.0514
2 0.5 0.0050 0.0108 0.0521
5 0 0.0057 0.0094 0.0509
5 0.5 0.0046 0.0094 0.0496
Dichotomous 0.01 2 0 0.0050 0.0107 0.0488
2 0.5 0.0039 0.0082 0.0472
5 0 0.0059 0.0108 0.0499
5 0.5 0.0045 0.0089 0.0465
0.05 2 0 0.0065 0.0125 0.0529
2 0.5 0.0049 0.0108 0.0477
5 0 0.0053 0.0115 0.0525
5 0.5 0.0046 0.0093 0.0480
  1. The empirical type-I errors were estimated using 10,000 replicates at several significance levels. We assumed that the number of markers is two, and that their minor allele frequencies were generated as U(0.1, 0.5). The phenotypic correlations were assumed to be 0.2.