This could possibly lead to a larger deviance statistic under the null hypothesis and the global permutation p-value would then be too large (conservative).
But how likely is a large dominance deviance?
Thus, the chance of a large dominance deviance is even less when testing at a noncausal locus, suggesting that use of genotypic tests must be carefully considered and that the comparison between tests in the presence of low dominance deviance is of the greatest practical importance.
Such a bi-modality may increase the time to convergence of the Markov Chain Monte Carlo (MCMC) sampling and result in poor model fits (ie, large deviance information criterion, DIC).
In contrast, the current study did not result in a significant difference between conditions of smaller and larger deviance size.
In humans and other animals, the MMN amplitude and latency have been shown to be dependent on the magnitude of stimulus deviance [14]; a large variation between standard and deviant stimuli evokes a larger MMN amplitude.
For large positive dominance deviance (suggesting a large dominant genetic effect), the dominant tests EGD and GDE are strictly optimal, closely followed by the genotypic tests EGG and GGE.
The first fit of the log linear model (Model 1) found that patch contributed the greatest effect (LRT6 = 1891.405, mean deviance >1; p<0.0001), but a large proportion of the residual variance remained unexplained (Table 2).
A classic age-period-cohort model showed considerably better model fit, with a large and significant decline in model deviance (−20 078 with 178 fewer degrees of freedom, P<0.001, table 1) compared with using a combined breast cancer rate for all age groups, cohorts, and periods.
Elsewhere, Urakawa et al. [78] used MEG to examine visual deviance detection and demonstrated a large middle occipital gyrus response to infrequent stimuli that was followed by activation in the precuneus and right IFG in three out of eight participants.
