Re: Maternal Genetic effects in ASReml-R

Dear Arthur/Bruce,

Sorry, I should have made it clearer. The design I explained is only
a single replicate within a larger experiment (each experiment has
100 of these replicates). I am now certain that the problem lies
with the model specification since the original model:

asreml(y~1, random=~nurse+ped(id, var=T)+ped(nurse, var=T), ginverse
(id=Gped, nurse=Gped))

can actually be reparameterised as:

asreml(y~1, random=~nurse+ped(id, var=T)+dnurse, ginverse(id=Gped))

where dnurse is the dam identifier of the nurse. This gives unbiased
variance estimates where

nurse = Maternal environment + 0.5Maternal genetic

and

dnurse = 0.5Maternal genetic

so I am confident the design is adequate. Is it possible that asreml-
r is not associating the nurse identifiers with the G inverse? The
estimates suggest that "ped(nurse, var=T)" is specifying the same
structure as "nurse".

Also, I cannot seem to get the link function working for this type of
model - the manual says that the implementation of link is still not
finished so this may be the problem?

I realise that these models are straightforward in stand alone
ASReml, but we are running a course on evolutionary quantitative
genetics at the end of the month and we had hoped to do everything
through the R interface, as it will be easier for the uninitiated.

Thanks for the help,

Jarrod

On 1 Feb 2008, at 19:56, arthur.gilmour_at_DPI.NSW.GOV.AU wrote:

>
> Dear Jarrod,
>
> Let me add my thoughts.
>
> It would appear that the design is adequate, otherwise you would
> generate a singularity in the AI matrix.
>
> However, the data set is small so it is highly likely that sampling
> variation could generate the result you have observed.
> If you have generated 100 samples and they all show this feature,
> then maybe there is a problem with the simulation.
>
> Just check that you have the correct number of effects fitted.
>
> One check of coding is to export the data frame and run the job in
> standalone ASReml (which uses the same license).
>
>
>
>
> May Jesus Christ be gracious to you in 2008,
>
> Arthur Gilmour, His servant .
>
> Mixed model regression mapping for QTL detection in experimental
> crosses. Computational Statistics and Data Analysis 51:3749-3764
> at http://dx.doi.org/10.1016/j.csda.2006.12.031
>
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> NSW Department of Primary Industries
> Orange Agricultural Institute, Forest Rd, ORANGE, 2800, AUSTRALIA
>
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> ><><><><><><><><><><><><><><><><><><><><><><><>
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>
> Jarrod Hadfield <J.Hadfield_at_ED.AC.UK>
> Sent by: ASReml users discussion group <ASREML-L_at_AGRIC.NSW.GOV.AU>
> 01/02/2008 06:52 AM
> Please respond to
> ASReml users discussion group <ASREML-L_at_AGRIC.NSW.GOV.AU>
>
> To
> ASREML-L_at_AGRIC.NSW.GOV.AU
> cc
> Subject
> Re: Maternal Genetic effects in ASReml-R
>
>
>
>
>
> Dear Brian,
>
> Thanks for the quick reply. I haven't been able to get correlated
> random effects using "link" yet (I get various error messages), but
> I'm not sure I've specified ASReml-R to fit the simpler model
> correctly.
>
> I am using simulated data in order to test the power of different
> designs for estimating maternal genetic effects, and I'm reasonably
> confident that the design I have allows me to separate additive
> genetic, maternal additive genetic and maternal environment
> effects. However when I fit the model the maternal environment
> effect is constrained at zero. The estimate of the additive
> genetic variance seems to be unbiased but the estimate of the
> maternal genetic variance is equal to the total maternal variance
> (genetic + maternal):
>
> The model I fit is:
>
> asreml(y~1, random=~nurse+ped(id, var=T)+ped(nurse, var=T), ginverse
> (id=Gped, nurse=Gped))
>
> but the estimates suggest that nurse and ped(nurse, var=T) are
> fitting the same thing (allthough they are not).
>
> The replicates consist of 4 pairs of sisters mated to 8 unrelated
> males to form 8 parental pairs. Each of the 8 parental pairs then
> produce 4 offspring. The 8 parental pairs are then organised into 4
> dyads where the 2 pairs making up the dyad are unrelated to each
> other. 1/2 of the offspring for each pair are reared by the other
> parental parents within the dyad. Offspring are therefore raised
> by nurses, which in 50% of cases are also their dams. In addition
> the dyads are formed so that a sister pair are not paired with
> individuals that are also sisters. Hence, I'm reasonably confident
> the effects can be estimated since unrelated offspring are reared
> by sisters (maternal genetic effects), unrelated offspring are
> reared by the same nurse (maternal environmental effects) and
> related offspring are reared by their mothers and unrelated nurses
> (additive genetic effects).
>
> Perhaps I'm mistaken?
>
> Jarrod
>
>
>
>
>
>
> On 30 Jan 2008, at 17:20, brian.cullis_at_DPI.NSW.GOV.AU wrote:
>
>
> Dear jarrod
> I have to admit that I have never fitted these but I would imagine
> that you could as shown in the ASReml-R manual page 58 section 5.4.
> As for correlating additive and maternal I would think this is also
> possible using us(link(~ped(Calf) + ped(Dam))) but I dont think
> this has been tested or requested. Hence I am ccing this to David
> Butler, the author of ASReml-R to check the syntax and the use of
> ped() within link()
>
> Arthur and I are in the UK at the moment and so DBs response will
> be in Oz time
>
>
> warm regards
>
> Brian Cullis
> Research Leader, Biometrics &
> Senior Principal Research Scientist
> NSW Department of Primary Industries
> Wagga Wagga Agricultural Institute
>
> Professor,
> Faculty of Agriculture, Food & Natural Resources
> The University of Sydney
>
> Phone: 61 2 6938 1855
> Fax: 61 2 6938 1809
> Mobile: 0439 448 591
>
>
>
>
> Jarrod Hadfield <J.Hadfield_at_ED.AC.UK>
> Sent by: ASReml users discussion group <ASREML-L_at_AGRIC.NSW.GOV.AU>
> 31/01/2008 04:02 AM
> Please respond to
> ASReml users discussion group <ASREML-L_at_AGRIC.NSW.GOV.AU>
>
>
> To
> ASREML-L_at_AGRIC.NSW.GOV.AU
> cc
> Subject
> Maternal Genetic effects in ASReml-R
>
>
>
>
>
>
>
> Hi Everyone,
>
> Is it possible to fit maternal genetic effects in ASReml-R yet? If
> so does any one have any example code they could show me (preferably
> with the covariance between additive and maternal genetic effects
> estimated)?
>
> Thanks,
>
> Jarrod
>
>
Received on Tue Feb 02 2008 - 13:33:27 EST