Thanks to Dr. Gilmour, Apiolaza adn Dutkowski for your help.
The following is the answer by Dr. Gilmour. Sorry I did not forward
before. I was out of town these days.
I tried Dr. Gilmour suggestions. They work as he said.
Thanks again.
Uilson
---------- Forwarded message ----------
Date: Mon, 20 Jul 1998 08:01:58 +1000 (EST)
From: Arthur Gilmour <gilmoua@ornsun.agric.nsw.gov.au>
To: wilsonvl@grove.ufl.edu
Subject: Re: true BLUP
Dear Uilson,
There are two points to understand.
1 When using the !GF option, it must be specified for every parameter.
Thus the job would be like
True BLUP
env 2 # environments
fam 80 # families
blk 12 # blocks
x1
/f/share/uvl/CHAP3/BLUPtrue/CH3e.dat !maxit 1
x1 ~ mu blk env !r fam 0.0013468 !GF fam.env 0.052304 !GF blk.fam 0.11188 !GF
1 1 0
0 !S2==0.012249 # !GF
If you look at the results below, you will see that the Error variance was
fixed in BOTH (!S2== fixes it).
The !GF is not needed on that line because there are no other parameters for it
to apply to.
Another way of writing the last line is
0 0 0 0.012249 !GF !S2==1
The blk.fam variance was also fixed in that second run
because the !GF followed 0.11188
>
2. Both analyses are giving you the 'true blup'
BLUP referes to the character of the random effects.
The random effects reported after the first iteration
are calculated using the parameter values used in that iteration,
the once that were input. ASREML then provides REML updates of
those parameters and would use the updated parameters in the
second iteration. The !GF procedure therefore alters
the REML part of the process but not the BLUP part.
I.e. The numbers in the .sln file are not altered by the
presence or absence of !GF in the .as file [after the first
iteration]. This comment may not apply to the Variance parameter
fixed by the !S2== clause in that if you used !S2= instead, the
SEs of the BLUPS might change in the .sln file. You could confirm
that.
I trust this helps
PS You would need to add the !GF qualifiers to Luis version of your job to
fix the parameters. If you succeed in fixing the parameters, you could omit
the !MAXIT 1
and allow ASREML to do 2 iterations when it would stop because there is no
change in the LogL.
Arthur
> From: Uilson V Lopes <wilsonvl@grove.ufl.edu>
> Comments: PAA01154 on bay (hop 0), Fri, 17 Jul 1998 15:44:30 -0400 (EDT)
> Date: Fri, 17 Jul 1998 15:44:30 -0400 (EDT)
> X-Sender: wilsonvl@bay
> To: asreml@ram.chiswick.anprod.csiro.au
> Subject: true BLUP
> MIME-Version: 1.0
>
> Dear asremlrs,
> Sorry to return to the TRUE BLUP problem.
>
> I am trying to run true BLUP in a simulated data set.
>
> I tried the option !maxit, but the final variance components are different
> from my priors (Analysis 1, below).
>
> Then I tried to add the option !GF, which was supposed to keep fixed the
> variance components. Again, the estimates of the variance components are
> different from my priors (Analysis 2, below).
>
> Could somebody help me solve this?
> Thanks
> Uilson Lopes
>
>
>
> ====================================
> .as file
>
> True BLUP
> env 2 # environments
> fam 80 # families
> blk 12 # blocks
> x1
> /f/share/uvl/CHAP3/BLUPtrue/CH3e.dat !maxit 1
> x1 ~ mu blk env !r fam 0.0013468 fam.env 0.052304 blk.fam 0.11188 # !GF
> 1 1 0
> 0 !S2==0.012249 # !GF
>
> ======================================================
> ANALYSIS 1. NO !GF option
>
>
> LogL=-285885. S2= 0.1225E-01 9588 df 0.00135 0.05230 0.11188
> 0.01225
> Final parameter values 0.00549 0.06940 0.14017
> 0.01225
>
> Source Model terms Gamma Component Compnt/StndErr
> fam 80 80 0.549387E-02 0.549387E-02 0.84
> fam.env 160 160 0.694019E-01 0.694019E-01 7.33
> blk.fam 960 960 0.140167 0.140167 28.44
> Variance 9600 9588 0.122490E-01 0.122490E-01 0.00
> =====================================================
> ANALYSIS 2. WITH !GF option
>
> LogL=-285885. S2= 0.1225E-01 9588 df 0.00135 0.05230 0.11188
> 0.01225
> Final parameter values 0.00549 0.07412 0.11188
> 0.01225
>
> Source Model terms Gamma Component Compnt/StndErr
> fam 80 80 0.549387E-02 0.549387E-02 0.84
> fam.env 160 160 0.741164E-01 0.741164E-01 7.86
> blk.fam 960 960 0.111880 0.111880 0.00
> Variance 9600 9588 0.122490E-01 0.122490E-01 0.00
>
> ============================================================
>
<><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
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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