Dear Hugo,
Negative variance estimates are not uncommon.
COnsider a simple balanced sire model for which
an appropriate analysis of variance is
Source df MS E[MS]
SIRES s-1 SireMS Ve + kVs
ERROR n-s ErrorMS Ve
In this ANOVA, the SIRE and ERROR Mean squares are independent.
If Vs is small, it is quite likely that SireMS will be smaller than
ErrorMS. If you estimate Vs by equating meansquares to their expectation,
[SireMS - ErrorMS]/k will be negative and this is what unconstrained REML
will give for the Sire variance component.
Constrained REML would estimate Ve as [(n-s)*ErrorMS + (s-1)*SireMS]/(n-1)
and Vs as 0.
In your example, it appears there is no maternal variance.
I suggest you proceed to drop mat and pe from the model. I expect
a negligible decrease in LogL indicating there is no meaningful
maternal variance [either genetic or environmental]
It is possible that the maternal genetic component would increase if
pe is dropped from the model but I do not think it will increase enough to
become positive
Best wishes
Arthur
>
>
> Hello:
>
> With this .as file
>
> Birth weight
> ani !P
> mat !P
> pe 6803
> sex 2 !A
> aod
> aod2
> sy 50 !A
> AdG
> AdPH
> AdRA
> AdS
> AmS
> Dd
> Dm
> bw
> PE2_2.prn !MAKE
> BW21.prn
> bw ~ mu sex aod aod2 sy AdG AdPH AdRA AdS AmS Dd Dm !r ani mat pe .254
> 0 0 1
> ani 2
> 2 0 US 1.16 .0 .287
> ani
>
> I got this estimates for variances and covariances:
>
> Source Model terms Gamma Component Compnt/StndErr
> pe 6803 1572 0.781423E-03 0.805809E-02 0.02
> Variance 3132 3099 1.00000 10.3121 19.76
> ani US=UnStr 1 0.311831 3.21562 5.15
> ani US=UnStr 1 0.188442E-01 0.194323 0.64
> ani US=UnStr 2 -0.207402E-02 -0.213874E-01 -0.06
>
> I have two questions:
>
> 1) It is possible to obtain negative variance estimates with the REML
> algorithm
> used in ASREML? (i.e., this is something that you can expect in some
> situations?)
>
> 2) There is something wrong in my model setting that may explain the
> negative estimate?
>
> Thank you again
>
> Hugo
> ================================
> Hugo Montaldo
> Research Fellow
> Division of Animal Science
> University of New England
> Armidale, NSW 2351
> Australia
>
> Phone 61 2 67 733004
> Fax 61 2 67 733275
>
> E-mail hmontald@metz.une.edu.au
> http://metz.une.edu.au/~hmontald/
> ==================================
> "Volver a los diecisiete despues
> de vivir un siglo
> es como descifrar signos sin ser
> sabio competente"
> -Violeta Parra
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Arthur Gilmour PhD email: Arthur.Gilmour@agric.nsw.gov.au
Senior Research Scientist (Biometrics) fax: <61> 2 6391 3899
NSW Agriculture <61> 2 6391 3922
Orange Agricultural Institute telephone work: <61> 2 6391 3815
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