From: <fmujibi_at_UALBERTA.CA>

Date: Thu, 28 May 2009 14:42:21 -0600

Date: Thu, 28 May 2009 14:42:21 -0600

Thanks Authur for your response.

Much appreciated

-- Denis Fidalis Mujibi 1430 College Plaza 8215 112 St, Edmonton T6G 2C5, AB, Canada. fmujibi_at_ualberta.ca Quoting "Arthur Gilmour" <arthur.gilmour_at_CARGOVALE.COM.AU>: > Dear Denis, > > The estimated variance parameters need to be treated with caustion as > follows. > > First, the ? means that when ASReml calculates an AI update, the > result is not positive defiite so must be rejected. ASReml then > performs an EM type of update but EM updates take a long time to > converge. > > In this case, it is the SIRE term that is having trouble. > But the final parameters are > > Covariance/Variance/Correlation Matrix UnStructured Trait.sire > 0.6037E-01 0.8908 > 0.3931 3.225 > > which does not reveal a correaltion of almost 1, or a variance almost > zero, so it has not converged to a boundary condition. > [In general (for more than 2 traits, check the eigen values in the .res > file)] > > Often, you could specify the !PXEM qualifier and it might converge > faster. > Since you are using a pedigree for SIRE though, this may not work. > > The problem is like trying to climb mount Everest when you are not > allowed into Nepal. REML wants to locate the maximum REML likelihood > associated with the data and model, but you have said the SIRE matrix > must be positive definite and the highest REML LogL is associated with a > sire matrix that is not positive definite. > > So, all you can do, is try and find the highest point along the > boundary. > > Since it is a small data set, (512 individuals), the sire variance > matrix may not be well estimated (how many actual sires are there). > > So, in this case, the SIRE matrix is not almost singular (on the > boundary of the parameter space) so (much) more iteration is required. > > > On Tue, 2009-05-26 at 12:50 -0600, fmujibi_at_UALBERTA.CA wrote: >> Hello All. >> I am wondering about the validity of the variance components obtained >> when parameters converge at the boundary. (ASreml gives a warning >> message "? - liable to change from P to B"). Despite the fact that >> standard errors are not obtained, do the estimates still stand? >> >> Attached is a truncated version of the .asr file that I get >> >> Folder: C:\Documents and Settings\User\Desktop\Final_Formats >> id !P >> sire !P >> dam !P >> breed 4 !I >> group 3 !I >> A-inverse retrieved from ainverse.bin >> PEDIGREE [testdata.csv ] has 1014 identities, 2433 Non zero elements >> QUALIFIERS: !SKIP 1 !EXTRA 90 !MAXIT 100 !MVINCLUDE >> Reading testdata.csv FREE FORMAT skipping 1 lines >> >> Bivariate analysis of vfa and fwd100 >> Using 512 records of 512 read >> >> Model term Size #miss #zero MinNon0 Mean MaxNon0 >> 1 id !P 1014 0 0 1.000 491.3 1014. >> 2 sire !P 1014 33 0 1.000 235.3 1013. >> 3 dam !P 1014 40 0 34.00 438.9 1010. >> 4 breed 4 33 0 1 2.6931 4 >> 5 group 3 33 0 1 2.1315 3 >> 6 age 33 0 161.0 240.5 332.0 >> Warning: Fewer levels found in vfa than specified >> 7 vfa 50 33 2 -3 0.0082 3 >> 8 stpws50 0 0 -2.486 0.9287 5.230 >> 9 fwd100 Variate 0 0 -3.493 1.972 9.896 >> 10 bwd50 17 0 -1.833 0.2840 2.468 >> 11 st50blp 17 0 -2.578 0.2707 3.205 >> 12 Trait 2 >> 13 at(Trait,1) 1 >> 14 at(Trait,1).age 1 13 at(Trait,1: 1 6 age : 1 >> 15 at(Trait,1).breed 4 13 at(Trait,1: 1 4 breed : 4 >> 16 at(Trait,1).group 3 13 at(Trait,1: 1 5 group : 3 >> 17 Trait.sire 2028 12 Trait : 2 2 sire : 1014 >> Warning: 330 missing values were detected in the design variables >> Missing values are treated as zeros >> Consider deleting the records in which they occur >> 512 identity >> 2 UnStructure 0.7900 0.4000 2.1000 >> 1024 records assumed pre-sorted 2 within 512 >> 2 UnStructure 0.0800 0.2000 2.8500 >> 1014 Ainverse >> Structure for Trait.sire has 2028 levels defined >> Forming 2038 equations: 10 dense. >> Initial updates will be shrunk by factor 0.100 >> Notice: Algebraic ANOVA Denominator DF calculation is not available >> Numerical derivatives will be used. >> Notice: 2 singularities detected in design matrix. >> 1 LogL=-697.455 S2= 1.0000 983 df >> 2 LogL=-687.781 S2= 1.0000 983 df >> 3 LogL=-666.246 S2= 1.0000 983 df >> Notice: US matrix updates modified 1 time(s) to keep them positive definite. >> 4 LogL=-654.848 S2= 1.0000 983 df : 3 components constrained >> Notice: US matrix updates modified 1 time(s) to keep them positive definite. >> 5 LogL=-653.056 S2= 1.0000 983 df : 3 components constrained >> Notice: US matrix updates modified 1 time(s) to keep them positive definite. >> 6 LogL=-653.028 S2= 1.0000 983 df : 3 components constrained >> Notice: US matrix updates modified 1 time(s) to keep them positive definite. >> 7 LogL=-653.016 S2= 1.0000 983 df : 3 components constrained >> Notice: US matrix updates modified 1 time(s) to keep them positive definite. >> 8 LogL=-653.005 S2= 1.0000 983 df : 3 components constrained >> Notice: US matrix updates modified 1 time(s) to keep them positive definite. >> 9 LogL=-652.996 S2= 1.0000 983 df : 3 components constrained >> Notice: US matrix updates modified 1 time(s) to keep them positive definite. >> 10 LogL=-652.988 S2= 1.0000 983 df : 3 components constrained >> Notice: US matrix updates modified 1 time(s) to keep them positive definite. >> 11 LogL=-652.981 S2= 1.0000 983 df : 3 components constrained >> Notice: US matrix updates modified 1 time(s) to keep them positive definite. >> 12 LogL=-652.975 S2= 1.0000 983 df : 3 components constrained >> 13 LogL=-652.969 S2= 1.0000 983 df : 3 components constrained >> 14 LogL=-652.964 S2= 1.0000 983 df : 3 components constrained >> 15 LogL=-652.960 S2= 1.0000 983 df : 3 components constrained >> 41 LogL=-652.921 S2= 1.0000 983 df : 3 components constrained >> Notice: US structures were modified 38 times to make them positive definite. >> If ASReml has fixed the structure [flagged by B], it may not have >> converged to a maximum likelihood solution. >> !EMFLAG 0 Single standard EM update when AI update unacceptable >> >> Source Model terms Gamma Component Comp/SE % C >> Residual UnStructured 1 1 0.827632 0.827632 15.03 0 P >> Residual UnStructured 2 1 0.883629 0.883629 11.06 0 P >> Residual UnStructured 2 2 2.15469 2.15469 13.76 0 P >> Trait.sire UnStructured 1 1 0.603739E-01 0.603739E-01 0.00 0 ? >> Trait.sire UnStructured 2 1 0.393079 0.393079 0.00 0 ? >> Trait.sire UnStructured 2 2 3.22522 3.22522 0.00 0 ? >> Warning: Code B - fixed at a boundary (!GP) F - fixed by user >> ? - liable to change from P to B P - positive definite >> C - Constrained by user (!VCC) U - unbounded >> 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. >> Covariance/Variance/Correlation Matrix UnStructured Residual >> 0.8276 0.6617 >> 0.8836 2.155 >> Covariance/Variance/Correlation Matrix UnStructured Trait.sire >> 0.6037E-01 0.8908 >> 0.3931 3.225 >> >> Analysis of Variance NumDF DenDF F_inc Prob >> 12 Trait 2 NA 149.34 NA >> 14 at(Trait,1).age 1 496.8 0.27 0.605 >> 15 at(Trait,1).breed 3 735.8 3.16 0.026 >> 16 at(Trait,1).group 2 473.3 4.34 0.015 >> Notice: The DenDF values are calculated ignoring fixed/boundary/singular >> variance parameters using numerical derivatives. >> 17 Trait.sire 2028 effects fitted ( 740 are zero) >> >> >> > -- > Best Wishes, > Arthur Gilmour > > 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 > > http://www.CargoVale.com.au/ASReml > > Travel: > Brazil Jul27 - Aug 8 > UK Aug 10-14 > Mumbai Aug 16-17 > > This message is intended for the addressee named and may contain > confidential information. If you are not the intended recipient, > please delete it and notify the sender. Views expressed in this > message are those of the individual sender, and are not necessarily > the views of their organisation. > >Received on Fri May 28 2009 - 14:42:21 EST

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