[R] Differences between MTDFReml and kinship2

David Duffy David.Duffy at qimr.edu.au
Thu Nov 6 23:45:59 CET 2014

> From: "silvano" <silvano at uel.br>
> I fitted a genetic model using kinship2 and I compared it with MTDFReml program output.
> The residual variance of both are very close but the genetic variance are very differents.
> The output are:
> MTDFReml:
> genetic variance = 1.24015
> residual variance = 5.93424
> R (Kinship2):
> genetic variance = 0.767187
> residual variance = 5.6712
> Both of them use REML method. Could someone tell why the difference?

Hi Silvano.

You haven't given us enough information, I'm afraid.  We would need the
commands you used, the versions of the software,  plus output from both
jobs, and your data, or a smaller subset that exhibits the same problem.

You may have made an error, there may be a problem in one program, or the
likelihood might be flat around those solutions (ie your data are not very

It might be better to continue this on the R-sig-mixed-models list.

Cheers, David Duffy.

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