TABLE 3

Type I error rates for simulations of different models and tests for significance

Significance level
ModelSignificance testα = 0.10α = 0.05α = 0.01
Mixed modelGene dropping0.110 ± 0.01400.066 ± 0.01110.010 ± 0.0044
Permutation0.104 ± 0.01370.064 ± 0.01090.012 ± 0.0049
RegressionGene dropping0.136 ± 0.0153a0.072 ± 0.01160.018 ± 0.0059
Permutation0.914 ± 0.0125b0.812 ± 0.0175b0.518 ± 0.0223b
  • The type I error rates (mean ± standard error) were estimated from 500 simulations with thresholds being estimated from 5000 simulations separately for each model.

  • a The desired type I error rate falls outside of the 95% confidence interval.

  • b The desired type I error rate falls outside of the 99% confidence interval.