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Table 3 Type I error rates of different models in simulations

From: Large-scale transcriptome sequencing in broiler chickens to identify candidate genes for breast muscle weight and intramuscular fat content

Heritability

LASSO

EN

RR

LMM

Min (P)

Min

1SE (P)

1SE

Min (P)

Min

1SE (P)

1SE

Min (P)

1SE (P)

0.01

0

0

0

0

0

0.02

0

0

0.21

0

0

0.02

0

0

0

0

0.01

0.11

0

0

0.36

0.04

0

0.03

0

0

0

0

0.01

0.11

0

0

0.36

0.04

0

0.04

0

0

0

0

0

0.03

0

0

0.19

0.01

0

0.05

0

0.02

0

0

0.02

0.05

0

0

0.23

0.03

0

0.06

0

0.01

0

0

0.02

0.06

0

0

0.27

0.03

0

0.08

0

0.01

0

0

0.01

0.07

0

0

0.26

0.04

0

0.10

0

0

0

0

0

0.06

0

0

0.31

0.03

0

0.12

0

0

0

0

0

0.04

0

0

0.30

0.03

0

0.14

0.01

0.01

0

0

0.02

0.03

0

0

0.23

0.03

0

0.16

0

0

0

0

0.01

0.02

0

0

0.22

0.01

0

0.18

0

0.01

0

0

0.01

0.04

0

0

0.31

0.05

0

0.20

0

0

0

0

0

0.01

0

0

0.28

0.02

0

0.22

0

0

0

0

0

0.01

0

0

0.24

0.03

0

0.24

0

0.01

0

0

0

0.02

0

0

0.25

0.04

0

0.26

0

0

0

0

0

0

0

0

0.24

0.02

0

0.28

0

0

0

0

0

0.02

0

0

0.20

0.05

0

0.30

0

0

0

0

0

0

0

0

0.25

0.02

0

0.34

0

0.02

0

0

0

0.02

0

0

0.22

0.04

0

0.38

0

0

0

0

0

0

0

0

0.25

0.03

0

0.42

0

0.02

0

0

0

0.02

0

0

0.25

0.06

0

0.46

0

0

0

0

0

0

0

0

0.20

0.03

0

0.50

0

0.02

0

0

0

0.03

0

0

0.32

0.08

0

  1. LASSO: least absolute shrinkage and selection operator; EN: elastic net; RR, ridge regression; LMM: linear mixed model; Min: tuning parameters determined by minimizing cross validated mean squared prediction error; 1SE: tuning parameters in the model determined based on one standard error rule; P: p-value threshold were used for statistical significance, which was 0.05/15092 for LMM, and 0.05 for LASSO, EN, and RR