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Table 1 Comparison of the prior specifications in the eight MCMC chains A-H used to analyse the QTLMAS XII data, posterior estimates of model parameters and summary statistics

From: Impact of prior specifications in a shrinkage-inducing Bayesian model for quantitative trait mapping and genomic prediction

 

Prior specification

Posterior mean (sd) of

  

Chain

p 0

b (a)

N Q

α

1 0 2 σ u 2

σ 2

hM2 (b)

N Q

A

0.99

0.01

58.9

2.0 (0.6)

1.7 (1.2)

3.0 (0.1)

0.32 (0.02)

23.0 (2.5)

B

0.99

0.01

58.9

2.6 (0.7)

1.7 (1.2)

3.0 (0.1)

0.32 (0.02)

22.9 (2.6)

C

0.99

0.001

58.9

2.3 (0.5)

3.0 (1.9)

3.0 (0.1)

0.30 (0.02)

31.5 (2.5)

D

0.99

0.001

58.9

2.6 (0.5)

3.0 (1.9)

3.0 (0.1)

0.29 (0.02)

31.1 (2.5)

E

0.999

0.01

5.9

2.1 (0.5)

1.9 (1.3)

3.0 (0.1)

0.31 (0.02)

15.3 (1.3)

F

0.999

0.01

5.9

2.8 (0.5)

2.1 (1.4)

3.0 (0.1)

0.31 (0.02)

14.3 (1.3)

G

0.999

0.001

5.9

1.9 (0.4)

3.9 (2.3)

3.1 (0.1)

0.28 (0.02)

21.5 (1.4)

H

0.999

0.001

5.9

2.0 (0.7)

3.7 (2.2)

3.1 (0.1)

0.28 (0.02)

22.6 (1.8)

  1. (a) given in units of phenotypic standard deviations (sd(Y)=2.10).
  2. (b) The true overall heritability of the trait is 0.30 [19].
  3. Hyper-parameter p0 defines the prior probability that the effect size lies in the interval of the spike, (−b,b). N Q is a summary statistic for the number of QTL (see text for details), α the common intercept in the regression, σ u 2 the variance component of the polygenic terms, σ2 the residual variance, and h M 2 the part of the heritability due to marker effects.