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
Two factor ANOVA in lme
2 messages · Nathaniel Street, Fernando Henrique Ferraz P. da Rosa
3 days later
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