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Secondary outcomes will be analysed using a mixed modelling strategy, accounting for between practice variability by defining practices as random effects.
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This mixed model strategy is appropriate to use in this case since there are observations from the same sites over time.
Instead our association results show that both genomic components and linear mixed models strategies cope well with the substructure of the data and yield similar results.
Consequently, analyses of concatenated data set were only performed using a mixed-model strategy.
To estimate the unknown fixed effects and unknown σa2 we used a mixed model Bayesian strategy [ 18].
For mixed modeling, Proc Mixed (SAS Institute Inc).
For all mixed models, we used a step-up strategy whereby fixed factors were added to the model sequentially.
An alternative strategy to fit mixed models is the penalized quasi-likelihood (PQL) approach [ 18, 19] (GLIMMIX macro in SAS) but this method provides highly biased estimates of mixed-effects parameters with binary responses [ 20, 21].
For genes with multiple eQTLs, the aggregate heritability from all eQTLs was estimated by fitting genotypes from multiple eQTL peak SNPs into the linear mixed model and then following the same strategy used for single SNPs.
In practical data sets with arbitrary relationships and fixed effects, choices are less obvious and guidelines to good sampling strategies in a mixed model setting are scarce.
It is possible to consider strategies that use mixed model or Bayesian approaches to predict weaning weight means for lambs in the reference classes in individual management groups as frequency-dependent combinations of overall, flock, and management group means.
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