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Table 3 Empirical false positive rate and true positive rate results for simulation II (Discrete Populations with Outliers)

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

Case control Testing SNP Trend GC PCA MDS RPCA- RPCA-
Difference Types      RHM PP
S1 Random SNPs 2.75 1.41 1.94 0.97 1.01 0.99
(2 populations, moderate) Differentiated SNPs 99.85 98.75 93.03 1.33 0.99 1.00
Causal SNPs 48.97 37.55 48.33 46.95 44.69 45.06
S2 Random SNPs 16.74 1.71 8.38 1.09 0.99 1.00
(2 populations, more extreme) Differentiated SNPs 100.00 100.00 100.00 6.91 1.14 1.29
Causal SNPs 49.94 14.09 44.77 32.81 30.07 30.21
S3 Random SNPs 3.40 1.12 1.65 1.08 1.06 1.06
(3 populations, moderate) Differentiated SNPs 100.00 99.99 63.28 1.36 1.02 1.02
Causal SNPs 48.85 31.61 46.72 45.81 43.29 43.89
S4 Random SNPs 21.35 1.15 9.82 1.10 0.92 0.97
(3 populations, more extreme) Differentiated SNPs 100.00 100.00 100.00 18.13 1.29 1.51
Causal SNPs 50.09 9.41 37.56 21.76 18.66 18.81
  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.