 <r-sig-mixed-models@r-project.org>

Dear all,



I'm trying to analyze the genetic correlation between two traits using a
bivariate normal distribution in MCMCglmm.

I have 32 strains with 3 replicates and 1 observation per replicate for
Trait1 and 3 replicates and 2 observations per replicate for Trait2. I
addition to the genetic variance-covariance matrix for Trait1 and Trait2, I
would like to get the residual variance for Trait1 and Trait2, as well as
the between replicate variance for Trait2.


Would anyone know if it would be possible to fit a between replicate random
effect to only one of the two traits in MCMCglmm?


I detailed 3 different methods I’ve been using below but none of them
appears satisfactory.



1/Fixing the between replicate variance to 1 for Trait1 (‘priorvarRep ‘ and
fix argument below) also results in fixed residual variances for Trait1 and
Trait2.



priorvarRep<-priorvar

diag(priorvarRep)<-c(1,diag(priorvarRep)[2])



priorm1 <-list(G=list(G1=list(V= priorvar,n=2), G2=list(V=
priorvarRep,n=2,fix=c(1,0))), R=list(V= priorvar,n=2))



m1<-MCMCglmm(Value~-1+Trait, random = ~ us(Trait):Strain, rcov = ~
idh(Trait):units, family = "gaussian", ,prior=priorm1, data = data)



2/ Fixing the residual variance of Trait1 to 1 results in very weird
results for the residual variance of Trait2.



Priorm2 <-list(G=list(G1=list(V= priorvar,n=2), G2=list(V= priorvar,n=2)),
R=list(V= priorvarRep,n=2,fix=c(1,0)))



3/Out of curiosity, I’ve also tried a model without fixing any variance.
The between replicate variance fitted for Trait1 is then pretty close to
the residual variance of Trait1, but this might be an artifact.

Priorm3 <-list(G=list(G1=list(V= priorvar,n=2), G2=list(V= priorvar,n=2)),
R=list(V= priorvar,n=2,fix=c(1,0)))





Thank you very much for your help.





Best regards,



Nicolas

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