Robust methods for population stratification in genome wide association studies

BMC Bioinformatics

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

Case	Testing SNP	Trend	GC	PCA	MDS	RPCA-	RPCA-
Control	Types					RHM	PP
Difference							PP
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
(no outliers)	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
(with outliers)	Causal SNPs	49.15	37.63	48.23	45.30	42.37	45.50

^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.

ISSN: 1471-2105