factor 1 - treatment FIXED (two levels) factor 2 - genotype RANDOM (160 genotypes in total)
I need a model that tells me whether the treatment, genotype and interaction terms are significant. I have been reading 'Mixed effects models in S' but in all examples the random factor is not in the main model - it is a nesting factor etc to specify the error structure. Here i need the random factor in the model.
I have tried this:
height.aov<-lme(height~trt*genotype,data.reps,random=~1|genotype,na.action=na.exclude)
but the output is nothing like that from Minitab (my only previous experience of stats software). The results for the interaction term are the same but F values for the factors alone are very different between Minitab and R.
This is a very simple model but I can't figure out how to specify it. Help would be much appreciated.
As background: The data are from a QTL mapping population, which is why I must test to see if genotype is significant and also why genotype is a random factor.
Thanks
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