. Author manuscript; available in PMC: 2012 Nov 1.

Published in final edited form as: Genet Epidemiol. 2011 Aug 4;35(7):679–685. doi: 10.1002/gepi.20618

Table I.

Inflation factors and type-1 error rates of CMC, WSS, aSum, SPWST and PWST using uncorrected test and permutation test under 3 different experiment designs

Testing methods	Experiment design	Inflation factor (and type-1 error rate at 0.05 and 0.01 significance levels) ^*
Testing methods	Experiment design	CMC	WSS	aSum	SPWST	PWST
Uncorrected Regular Test	RDM	1.008 (0.051,0.012)	NA	2.591 (0.161,0.056)	18.441 (0.995, 0.929)	8.848 (0.999, 0.889)
	LR	1.050 (0.048,0.008)	NA	2.294 (0.095,0.023)	18.121 (0.993,0.938)	8.420 (0.990,0.859)
	LCR	1.030 (0.045,0.009)	1.372 (0.095,0.025)	2.511 (0.120,0.035)	18.362 (0.994,0.927)	8.543 (1.000,0.897)

Final Permutation test	RDM	1.041 (0.054,0.012)	NA	0.999 (0.051,0.010)	0.999 (0.045,0.012)	1.001 (0.054,0.010)
	LR	1.006 (0.052,0.011)	NA	1.002 (0.052,0.011)	1.005 (0.050,0.011)	1.030 (0.053,0.011)
	LCR	1.018 (0.051,0.011)	1.013 (0.051,0.010)	0.987 (0.0530,0.010)	0.993 (0.050,0.011)	1.004 (0.051,0.011)

Each value is calculated from 2000 p-values obtained by simulations under the null.