Table 1 Comparison of seven different methods in predicting gene expression levels in the GEUVADIS data

From: Non-parametric genetic prediction of complex traits with latent Dirichlet process regression models

Threshold

ENET

BayesR

BVSR

LMM

MultiBLUP

rjMCMC

DPR

       

VB

MCMC

0.10

1061

809

486

1195

1098

1013

1163

1280

0.20

449

338

142

403

299

321

389

467

0.30

182

170

48

162

110

123

155

194

0.40

78

84

24

76

46

47

70

86

0.50

37

35

10

33

16

19

32

38

0.60

15

14

4

14

5

9

12

17

0.70

2

3

1

3

1

2

2

3

  1. To compare prediction performance, we counted the number of genes whose median R 2 across 20 replicates in the test set is above a given R 2 threshold. A larger number thus indicates better performance. For each given threshold, we colored the best method with red and the second best method with blue
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