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Table 4 Empirical false positive rate and true positive rate results for simulations III and IV (Admixed populations)

From: Robust methods for population stratification in genome wide association studies

Case Testing SNP Trend GC PCA MDS RPCA- RPCA-
Control Types      RHM PP
Difference       
Simulation III Random SNPs 2.09 0.91 0.90 0.89 0.91 1.10
(no outliers) Differentiated SNPs 97.16 94.29 1.12 1.09 1.09 1.10
Causal SNPs 49.22 36.88 45.09 45.06 44.64 44.10
Simulation IV Random SNPs 2.27 1.12 1.89 1.04 0.91 0.80
(with outliers) Differentiated SNPs 97.59 94.17 88.11 10.09 1.01 1.40
Causal SNPs 49.15 37.63 48.23 45.30 42.37 45.50
  1. aFor random SNPs and differentiated SNPs, the values in the table represent the empirical false positive rates; for causal SNPs, the values in the table represent the empirical true positive rates. The nominal false positive rate is 0.01. Note that the numbers in the table refer to percentages.