Permanent environment effects in covariance analysis

Dear all,

I'm trying to calculate genetic covariances for traits for which I have
repeated measurements. For some of those traits, the permanent
environment gets bounded to zero in univariate analysis, and in the
multivariate analysis if I don't fix PE to 0 for these traits, then the
model will not converge.
Hence my question is: for the PE, what make more sense: is it (1) to
keep the covariance between PE free to take any values because this
reflects the repeated measurements in the data or (2) set the covariance
to 0 because covariance between a variance and a null component does not
really make sense?

The choice in this quite affects the results, and I can't really get
which is the proper line of reasoning.

Many thanks in advance for any help,

All the best

Celine
Received on Fri Apr 23 2009 - 15:24:25 EST