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Table 2

From: Multifactor dimensionality reduction: An analysis strategy for modelling and detecting gene - gene interactions in human genetics and pharmacogenomics studies

(A). Original MDR analysis of unbalanced data.

Number of loci in model

Best candidate model

Average cross-validation consistency

Average prediction error

1

1

10

20.00%

2

7, 8

7

21.28%

3

3, 5, 10

5

22.90%

4

2, 3, 5, 10

4

26.60%

5

1, 4, 7, 8, 9

4

29.66%

Final model: locus 1 -- INCORRECT MODEL

(B). Alnalysis using threshold adjustment only.

Number of loci in model

Best candidate model

Average cross-validation consistency

Average prediction error

1

5

5

40.80%

2

4, 9

3

30.53%

3

4, 5, 7

7

31.74%

4

3, 5, 8, 10

4

36.60%

5

1, 2, 4, 5, 9

5

40.00%

Final model: loci 4 and 9 -- INCORRECT MODEL

(C). Analysis using threshold adjustment and balanced accuracy.

Number of loci in model

Best candidate model

Average cross-validation consistency

Average prediction error

1

8

6

49.50%

2

10, 5

4

45.75%

3

10, 5, 3

10

29.97%

4

10, 5, 3, 2

7

33.69%

5

10, 8, 5, 4, 3

6

41.86%

Final model: loci 3, 5, 10 -- CORRECT MODEL

(D). Analysis of over-sampled data.

Number of loci in model

Best candidate model

Average cross-validation consistency

Average prediction error

1

8

9

46.25%

2

5, 10

3

46.75%

3

3, 5, 10

10

25.84%

4

3, 5, 8, 10

7

29.83%

5

3, 5, 6, 8, 10

5

25.88%

Final model: loci 3, 5, 10 -- CORRECT MODEL

(E). Analysis of under-sampled data.

Number of loci in model

Best candidate model

Average cross-validation consistency

Average prediction error

1

6

5

60.00%

2

5, 10

10

32.56%

3

3, 5, 10

10

28.00%

4

3, 5, 7, 10

7

32.53%

5

3, 4, 5, 6, 10

4

39.95%

Final model: loci 3, 5, 10 -- CORRECT MODEL

(F). Analysis using misclassification error for model selection.

Number of loci in model

Best candidate model

Average classification error

1

1

20.00%

2

7, 8

18.79%

3

3, 5, 10

18.00%

4

2, 3, 5, 10

16.80%

5

1, 4, 7, 8, 9

15.60%

Final model: loci 1, 4, 7, 8, 9 -- INCORRECT MODEL