Re: EMFLAG option in ASReml-3

Dear Craig,

The !EMFLAG is correctly positioned.

It pertains only to US structures which have the !GP qualifier
and you have two of these.

It kicks in when ASReml performs the AI update of the matrix.
If the updated matrix is not positive definite, the AI update
is replaced with an EM update.

The various options control whether a locally accelareted EM update is
performed. The accelerated forms are not approriate if the direct
product is with a term which has a relationship matrix associated.

You do not specify a relationship matrix for Ind or Genotype.

The message 'Negative Sum of Squares' relates to estimating the residual
variance. It can occur if the variance matrices are a long way from
a reasonable value, or if they are negative definite, which should not
be the case with your job. It can also occur when a relationship matrix
is involved and the 'heritability' exceeds 1.

It can also occur if the model fully explains the data.

On Wed, 2009-11-18 at 16:18 +1000, Craig Hardner wrote:
>
>
> I have got an RR analysis where I am getting negative sum of squares
> (Please find code below). I am interested in seeing if the EMFLAG
> options can help (on the other hand I may not have enough data to do
> what I am thinking of).
>
>
>
> Nevertheless my question is about the syntax for using the EMFLAG. As
> you can see I have tried !EMFLAG 7 (I have also tried other numbers)
> but nothing seems to come up in the .asr file indicating that EM has
> been used (and the negative sums of squares appears and the run
> crashes).
>

-- 
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Adjunct Professor
School of Computing and Mathematics
Charles Sturt University
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