[R] Two factor ANOVA in lme

[Fernando Henrique Ferraz P. da Rosa]

nat writes:
> I want to specify a two-factor model in lme, which should be easy? 
> Here's what I have:
> 
> 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

        It seems your message didn't get any replies (at least none
posted to r-help). 

        I recentely adjusted such a model  (two effects, one fixed,
another random, with interaction effects) using lme. I used the
following command: 

 z1 <- lme(reacao ~ posicao,data=memoria,random=~1|subject/posicao)

        Where my model is 

         reacao = mu + posicao (fixed) + posicao*subject (random) +
subject (random)

         Beware though that minitab uses different estimation methods (in lme
itself you may use maximum likelihood other restricted m.l) and the
results need not to be the same.

 


--
Fernando Henrique Ferraz P. da Rosa
http://www.ime.usp.br/~feferraz