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*To*: richardm@calm.wa.gov.au*Subject*: Re: rescaling design matrix*From*: Arthur Gilmour <gilmoua@apollo.agric.nsw.gov.au>*Date*: Mon, 13 Mar 2000 12:23:01 +1100 (EST)*Cc*: asreml@chiswick.anprod.csiro.au*Reply-To*: Arthur Gilmour <gilmoua@apollo.agric.nsw.gov.au>*Sender*: asreml-owner@lamb.chiswick.anprod.csiro.au

re Peter Kube's question, ASREML no longer runs in MSDOS real mode [since Dec 98 I think]. The Windows version can access all the memory that is available. re the following: The problem is most likely related to the fact that the variance ratio has gone to 50,000 i.e. the genetic variation is 50 times larger than the residual variation. There is probably something odd in the data [or maybe you started with this high value and it promptly failed. With this data, you could just fit a FEMALE model oil ~ mu rep prov !r fem The variance ration (g) will then typically be less than 0.33 So if half sib h2 is 4 g/(1+g) will be less than 1. However, in this case it may be more than 0.33 In a tree model, the genetic variance is 4gS and the residual is S(1-3g) where S is the residaul variacne from the female model Now if g > 0.33, the residual S(1-3g) becomes negative. ASREML will want to constrain the residual to be +ve so it has gone to a very small value and then been fixed there. So, in this case it is probably a problem with the model rather than the scale of the data. If it was a scaling problem, you would rescale the oil variable [by say !*0.01 transformation]. However, the scale of oil in this case looks fine. Arthur In wh When you fit the tree model, you expect a variance ration 4 times larger > X-Authentication-Warning: lamb.chiswick.anprod.csiro.au: petidomo set sender to asreml-owner@lamb.chiswick.anprod.csiro.au using -f > From: richardm@calm.wa.gov.au > Date: Thu, 9 Mar 2000 15:54:40 +0800 > To: <asreml@chiswick.anprod.csiro.au> > Subject: rescaling design matrix > MIME-Version: 1.0 > > Hi all, > > I am attempting to run a simple univariate "tree" model. > > Asreml has put out a warning message : WARNING: 1 singularities in AI matrix. > The suggestion is then made that the design matrix be rescaled. I am a > little uncertain as to how this may be achieved. Can this be done from within > asreml? Any pointers in the right direction would be greatly appreciated. > > .as file is as follows > > Merridin P95 tree analysis > tree !p > fem 25 !I > male > rep 20 > prov 3 !a > oil > > > ellmer95.prn > ellmer95.prn > > oil~ mu rep prov !r tree > > > relevent part of .asr file is below: > > > ASREML [ 1 Jul 1999] Merredin P95 tree analysis > > 09 Mar 2000 11:49:27.360 8.00 Mbyte C:\asreml\ellmer95.as > A-inverse retrieved from ainverse.bin > PEDIGREE [ellmer95.prn ] has 1303 identities, 2581 Non zero elements > Reading ellmer95.prn FREE FORMAT skipping 0 lines > Univariate analysis of oil > Using 1278 records [of 1278 read from 1278 lines of ellmer95.prn > ] > Model term Size Type COL Minimum Mean Maximum #zero #miss > > 1 tree 1303 Direct 1 2.000 663.9 1303. 0 0 > > 2 fem 25 Factor 2 1 13.2574 25 0 0 > 3 male 1 Covariat 3 0.000 0.000 0.000 1278 0 > 4 rep 20 Factor 4 1 10.6729 20 0 0 > > 5 prov 3 Factor 5 1 2.2926 3 0 0 > > 6 oil 1 Variate 6 0.1000 2.653 5.900 0 0 > > Forming 1328 equations: 25 dense > Initial updates will be shrunk by factor 0.548 > NOTICE: 2 (more) singularities, > LogL=-506.043 S2= 0.19031E-04 1256 df 0.5090E+05 1.000 > LogL=-506.043 S2= 0.19019E-04 1256 df 0.5093E+05 1.000 > Final parameter values 50933. 1.0000 > WARNING: 1 singularities in AI matrix. > > Source Model terms Gamma Component Comp/SE % C > tree 1303 1303 50933.5 0.968694 25.06 0 P > Variance 1278 1256 1.00000 0.190188E-04 0.00 0 S > WARNING: Code B - fixed at a boundary (!GP) > C - Constrained by user (!CON) > S - Singular Information matrix > S means there is no information in the data for this parameter. > Very small components with Comp/SE ratios of zero sometimes indicate poor > scaling. Consider rescaling the design matrix in such cases > > Analysis of Variance DF F-incr F-adj StndErrDiff > 4 rep 20 35.83 8.03 0.1515 > 5 prov 2 6.99 6.99 0.2748 > > Solution Standard Error T-value T-prev > 5 prov > NB 0.721356E-01 0.299888 0.24 > WE -0.709678 0.295945 -2.40 -3.53 > 4 rep > > > > thanks in advance > > Richard > ======================================= > Richard Mazanec > Dept of Conservation and Land Management > CALMScience Division > Brain street, Manjimup, 6258. > Phone +61 8 9771 7995 Fax +61 8 9777 1183 > Email: richardm@calm.wa.gov.au > -- > Asreml mailinglist archive: http://www.chiswick.anprod.csiro.au/lists/asreml <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> Arthur Gilmour PhD mailto:Arthur.Gilmour@agric.nsw.gov.au Principal 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 ASREML is still free by anonymous ftp from pub/aar on ftp.res.bbsrc.ac.uk or point your web browser at ftp://ftp.res.bbsrc.ac.uk/pub/aar/ To join the asreml discussion list, send the message subscribe mailto:asreml-request@chiswick.anprod.CSIRO.au To send messages to the list, mailto:asreml@chiswick.anprod.CSIRO.au Asreml list archive: http://www.chiswick.anprod.csiro.au/lists/asreml <> <> <> <> <> <> <> "Christ Jesus came into the world to save sinners" I Timothy 1:15. <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> -- Asreml mailinglist archive: http://www.chiswick.anprod.csiro.au/lists/asreml

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