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Table 9 Mean and standard deviation of the Pearson correlation coefficient for the simulated database 2 groups with raw p-values.

From: SNPs selection using support vector regression and genetic algorithms in GWAS

Group

SNP selection with raw p-values*

# SNPs

Linear**

RBF**

PUK**

1

< 10-9

1a

0.53(0.07)

0.94(0.04)

0.95(0.04)

2

< 10-8

1a

0.53(0.07)

0.94(0.04)

0.95(0.04)

3

< 10-7

1a

0.53(0.07)

0.94(0.04)

0.95(0.04)

4

< 10-6

1a

0.53(0.07)

0.94(0.04)

0.95(0.04)

5

< 10-5

3b

0.53(0.07)

0.94(0.04)

0.95(0.04)

6

< 10-4

5

0.53(0.07)

0.94(0.04)

0.94(0.04)

7

< 10-3

15

0.53(0.07)

0.94(0.04)

0.95(0.04)

8

< 10-2

99

0.64(0.07)

0.68(0.06)

0.69(0.06)

9

< 10-1

995

0.66(0.06)

0.79(0.04)

0.80(0.04)

10

< 0.20

2,053

0.73(0.05)

0.80(0.03)

0.80(0.03)

11

< 0.30

3,079

0.74(0.04)

0.79(0.03)

0.79(0.03)

12

< 0.40

4,066

0.75(0.04)

0.78(0.04)

0.78(0.04)

13

< 0.50

5,033

0.74(0.04)

0.75(0.04)

0.76(0.04)

14

< 0.60

5,996

0.69(0.05)

0.71(0.05)

0.71(0.04)

15

< 0.70

6,950

0.63(0.05)

0.64(0.05)

0.65(0.05)

16

< 0.80

7,934c

0.51(0.07)

0.51(0.07)

0.53(0.07)

17

< 0.90

8,893c

0.33(0.10)

0.32(0.10)

0.33(0.10)

18

-

5d

0.53(0.07)

0.97(0.02)

0.99(0.01)

  1. *Raw p-values of the Spearman correlation (without Bonferroni correction).
  2. ** Mean and standard deviation of the Pearson correlation in 10-fold cross validation.
  3. (a) Only SNP3. (b) Contains SNPs 3, 4 and 5. (c) Contains SNPs 3, 4, 5, 9 and 12. (d) Only SNPs 3, 4, 5, 9 and 12.