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Table 7 Comparison of the power and false positive proportions of KWII to MDR, RPM, and regression approaches.

From: Comparison of information-theoretic to statistical methods for gene-gene interactions in the presence of genetic heterogeneity

Interaction

Sample Size

α

Power %

   

KWII

MDR

RPM

Logistic

Interaction 1

600

0.001

68.9

7.8

48.8

68.3

  

0.0001

42.2

3.7

29.5

43.3

 

1200

0.001

98.9

39.1

94.9

99.1

  

0.0001

95.6

10.0

87.8

95.4

 

2400

0.001

100

65.3

100

100

  

0.0001

100

13.8

100

100

Interaction 3

600

0.001

15.1

0.04

7.2

14.8

  

0.0001

4.8

0.03

3.2

5.2

 

1200

0.001

47.6

3.6

28.1

48.7

  

0.0001

26.6

0.04

15.2

24.6

 

2400

0.001

95.1

6.6

84.4

94.0

  

0.0001

83.5

0.05

70.8

84.2

All 3 Interactions

600

0.001

7.6

0.01

2.2

7.5

  

0.0001

15.2

0.01

0.5

14.1

 

1200

0.001

48.1

0.03

25.7

47.8

  

0.0001

26.6

0.01

11.5

22.1

 

2400

0.001

95.1

2.9

84.4

94.0

  

0.0001

83.5

0.01

70.8

84.2

Interaction

Sample Size

α*

Proportion of False Positives

   

KWII

MDR

RPM

Logistic

All 3 Interactions

600

0.001

-

0.0021

0.0010

0.0013

  

0.0001

-

0.0010

0.0001

0.0001

 

1200

0.001

-

0.0075

0.0013

0.0016

  

0.0001

-

0.0011

0.0003

0.0002

 

2400

0.001

-

0.0103

0.0009

0.0013

  

0.0001

-

0.0014

0.0002

0.0002

  1. *α is calibrated to the empirical false positive rate of KWII.
  2. The model used for the simulations contained three interacting pairs of SNP as summarized in Table 1: Interaction 1 and Interaction 2 in were based on [16] whereas Interaction 3 was based on [2].