Re: EMFLAG option in ASReml-3

From: Arthur Gilmour <arthur.gilmour_at_CARGOVALE.COM.AU>
Date: Thu, 19 Nov 2009 09:27:41 +1100

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).

Best Wishes,
Arthur Gilmour
Adjunct Professor
School of Computing and Mathematics
Charles Sturt University
Jesus went to the synagogue in every town in Galilee to preach and drive
out demons.
A leper came, knelt down and said, "If you will, you can make me clean".
Jesus was moved. He reached out and touched him and said 
"I am willing.  Be clean." He was cleansed immediately.
Mobile Number +61 427 227 468
Home phone +61 2 6364 3288  Skype: Arthur.Gilmour
By the way: listen to Alan Jones (2GB Radio) interview 
with Lord Mockton on the Copenhagen Summit 
Brisbane Probe 29Nov to 6 Dec
Bangladesh Proshikkon 31Dec - 6 Feb
Received on Fri Nov 19 2009 - 09:27:41 EST

This webpage is part of the ASReml-l discussion list archives 2004-2010. More information on ASReml can be found at the VSN website. This discussion list is now deprecated - please use the VSN forum for discussion on ASReml. (These online archives were generated using the hypermail package.)