Table 2 Type I error rates of four tests in a homogenous population and in the case of no population stratification for qualitative traits.

From: A Nonparametric Regression Approach to Control for Population Stratification in Rare Variant Association Studies

Population Structures

Test

Alpha

Un-corrected

GC

PC-linear

PC-nonp

A Homogenous Population

Single Variant

0.01

0.0131

0.0076

0.0129

0.01178

0.001

0.00168

0.00112

0.00182

0.00172

Regional

0.01

0.00992

0.00958

0.00992

0.0121

0.001

0.00124

0.00116

0.00122

0.00162

No Population Stratification

Single Variant

0.01

0.01082

0.0053

0.01

0.0079

0.001

0.00169

0.0007

0.00162

0.0014

Regional

0.01

0.0113

0.00904

0.01176

0.00926

0.001

0.00178

0.00138

0.00166

0.00134

  1. Note: “A homogenous population” means k0 = 1 in simulation set 1; “no population stratification” means model 0 in simulation set 2.
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