RE:Unreplicated analysis
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RE:Unreplicated analysis



Dear Vince,
You wrote.
> 	Assume we have an unreplicated trial with repeated checks. Now,
> for the analysis of such a trial i believe that the estimate of 'error'
> comes (or should) come from an ANOVA on the check plots. However, I have a
> suspicion that the error estimate is from an ANOVA on the checks and
> genotypes. 
> 
Your suspicions are wrong.  You can verify this from
doing the following series of analyses (without spatial
adjustement so you can see exactly what is happening).

1.  yeild ~ Check !r geno
    with all the data and Check having one level which
    is assocoated with testlines, other levels assoc with
    check varieties,  geno being the test lines (coded zero
    for check plots)
    
2.  yeild ~ Check
       dropping all the test-line data.  OR
    yeild ~ Check geno
       treating test lines as fixed effects and having all the data.
       
       
These two analyses should give exactly the same residual variance
[unless the geno variance goes to zero boundary in which
case you will need to allow it to go negative !GU] to get
the same error variance.

If replication is only in the Check lines and test lines are fitted,
the only information on the error variance comes from the check lines.

Now, consider the case where all genotypes are treated as random.
Then things will not work out so neatly becasue the variance of
the check lines is not likely to be the same as the variance of the test
lines. If checks were equireplicated and had their own variance,
things would work out but otherwise, the residual would change slightly.

When we go to a spatial analysis, again, all the information on error
correlation comes from the check plots.  This is why we recommend having a few
of the check plots additional to the regular grid spacing - so as to
get same lag 1 and lag 2 information as well as the lag5 information.

> Date: Mon, 13 Jul 1998 17:12:10 +1000 (GMT+1000)
> From: Vincenzo Matassa <s185152@student.uq.edu.au>
> To: asreml@ram.chiswick.anprod.csiro.au
> Subject: RE:Unreplicated analysis
> MIME-Version: 1.0
> 
> Dear All
> 	Assume we have an unreplicated trial with repeated checks. Now,
> for the analysis of such a trial i believe that the estimate of 'error'
> comes (or should) come from an ANOVA on the check plots. However, I have a
> suspicion that the error estimate is from an ANOVA on the checks and
> genotypes. 
> 
> The problem with the latter approach is that typically in unreplicated
> trials check plots will usually have a smaller variance than the random
> genotypes. Hence if we run an ANOVA on checks and geno's in order to
> estimate the error component for our trial it may be poorly (over or
> underestimated) estimated .
> 
> Is there a way in ASREML to just get the estimate of the error variance
> solely from an ANOVA on the checks when we fit a spatial model to our
> data    Yield ~ mu c(checks) !r genotypes ? 
>

If you fit genotypes as fixed effects, then that will remove any
contribution they might make.
 
> Many thanks for your help.
> 
> Kind regards
> 
> Vince
> 
> Vince Matassa 
> Department Of Agriculture
> BIOMETRICS SECTION 
> University Of Queensland 
> Brisbane 4072 
> Australia
> 
> 


<><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
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
Forest Rd, ORANGE, 2800, AUSTRALIA                    home: <61> 2 6362 0046

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