Mixed model analysis using lme4
I am a novice in using mixed models. I am not sure how to set up the fixed and random effects in mixed model. Your expertise would be much appreciated.
My experimental set up is as follows: Three years of experiment (Experiment), three nested-association-mapping families (Family) and within each family 50 lines making a total of 150 lines (Line). For each of the line, there are three replicates (Replicate). Several traits were measured (Trait).
So now I am not confident to define factors as fixed and which are random, which are to be nested within higher level grouping factor.
lmer (trait ~ (1|Genotype) + Experiment + (1:Replicate:Lines) + (1|Lines:Family) + (1|Family:Experiment)
Is this the correct way to do it?
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