Dear Listers,

Could anyone advise if this is the 'correct' contrast matrix to use to make contrasts between one treatment and the mean of 2 other treatments (in this case, mid-parent values to the F1 and F2 from a line cross experiment)?
Desired contrasts are
1) P1 versus P2
2) average of P1 and P2 versus F1
3) average of P1 and P2 versus F2
levels(MyData$Type)
"P1", "F1", "F2","P2"
(I have renamed these A, B, C, D in the actual data so they appear in the order above)
Contrast matrix:
contr_mat<-cbind(
 c(1,0,0,-1),
c(-1,2,0,-1),
c(-1,0,2,-1))

contrasts(MyData$Type)<-contr_mat

Model:
mod<-lm(Trait~Type,data=MyData)



Also, I would ideally like to run this in lme with a random effect for Block

mod2<-lme(Trait~Type,random=~1|Block,data=MyData)



Each treatment appears once in each block (ie balanced). Is there any problem using this contrast set-up in a mixed model? I am not sure how the 'block' effect would be interpreted for the mid-parent values, or indeed if it is sensible to include it as a random effect.



Thank you in advance for your help,



Rebecca Ross

University of Oxford









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