From: Arthur Gilmour <arthur.gilmour_at_CARGOVALE.COM.AU>

Date: Fri, 6 Nov 2009 15:53:10 +1100

Date: Fri, 6 Nov 2009 15:53:10 +1100

Dear Subhash,

The only evident difference between the runs is in the .sln file

where there will be extra ZERO solutions in the GROUP.ENTRY term

relative to the ENTRY term.

This is because GROUP is a classification of ENTRY.

For example

GROUP 1 has ENTRY 1 2; GROUP 2 has ENTRY 3 4

The models would be different if ENTRY was coded within GROUP.

For example

GROUP 1 has ENTRY 1 2; GROUP 2 has ENTRY 1 2

but the ENTRY 1 in GROUP 1 is not the same genotype as ENTRY 1 in GROUP

2

On Thu, 2009-11-05 at 14:03 -0600, KRISHNAMURTHY, SUBASH [AG/1000]

wrote:

*> All,
*

*>
*

*>
*

*>
*

*> I am fitting the following two models in ASREML. They are identical
*

*> except for the part highlighted in YELLOW. The two models produce
*

*> identical results. The first model is saying ENTRY is nested within
*

*> GROUP1 and in the second model, the two factors GROUP1 and ENTRY are
*

*> modeled as independent factors. Why would the two models produce
*

*> identical results?
*

*>
*

*>
*

*>
*

*>
*

*>
*

*> Model1
*

*>
*

*> !PATH 4 #MULTI LOC MULTI REP BLUE G1-Fixed ENTRY-FIXED
*

*>
*

*> tabulate RESPONSE ~ GROUP1 ENRTY
*

*>
*

*> RESPONSE ~ mu GROUP1/ENTRY !r LOC/REP LOC.GROUP1 LOC.REP.GROUP1
*

*>
*

*> predict GROUP1 !PRESENT GROUP1 ENTRY !SED !TDIFF
*

*>
*

*> predict GROUP1.ENTRY !SED !TDIFF
*

*>
*

*>
*

*>
*

*> Model2
*

*>
*

*> !PATH 4 #MULTI LOC MULTI REP BLUE G1-Fixed ENTRY-FIXED
*

*>
*

*> tabulate RESPONSE ~ GROUP1 ENRTY
*

*>
*

*> RESPONSE ~ mu GROUP1 ENTRY !r LOC/REP LOC.GROUP1 LOC.REP.GROUP1
*

*>
*

*> predict GROUP1 !PRESENT GROUP1 ENTRY !SED !TDIFF
*

*>
*

*> predict GROUP1.ENTRY !SED !TDIFF
*

*>
*

*>
*

*>
*

*>
*

*>
*

*> ASR file from Model1
*

*>
*

*>
*

*> ASR File from Model 2
*

*>
*

*>
*

*> ASReml 2.00b [01 Jul 2006] ASREML
*

*> GUBD MODULE
*

*>
*

*> Build: w [ 1 Oct 2008] 32
*

*> bit
*

*>
*

*> 05 Nov 2009 13:52:27.004 1264.00
*

*> Mbyte Windows
*

*> GUBD_Integrated_Module
*

*>
*

*> Licensed to: Monsanto
*

*>
*

*> ***********************************************************
*

*>
*

*> * SYNTAX change: A/B now means
*

*> A A.B *
*

*>
*

*> *
*

*> *
*

*>
*

*> * Contact support_at_asreml.co.uk for
*

*> licensing and support *
*

*>
*

*> ***************************************************** ARG *
*

*>
*

*> Approximate stratum
*

*> variance decomposition
*

*>
*

*> Stratum Degrees-Freedom
*

*> Variance Component
*

*> Coefficients
*

*>
*

*> LOC 3.00
*

*> 834.703 18.4 9.1 1.8
*

*> 1.0
*

*>
*

*> LOC.REP 4.02
*

*> 441.324 0.0 9.7 1.9
*

*> 1.0
*

*>
*

*> LOC.REP.GROUP1 27.93
*

*> 496.102 0.0 0.0 3.6
*

*> 1.0
*

*>
*

*> Residual Variance 131.05
*

*> 29.3327 0.0 0.0 0.0
*

*> 1.0
*

*>
*

*>
*

*>
*

*> Source Model terms
*

*> Gamma Component Comp/SE %
*

*> C
*

*>
*

*> LOC 4 4
*

*> 0.771952 22.6434 0.56
*

*> 0 P
*

*>
*

*> LOC.REP 8 8
*

*> 0.606630 17.7941 0.54
*

*> 0 P
*

*>
*

*> LOC.GROUP1 20 20
*

*> 0.535386E-07 0.157043E-05 0.00
*

*> 0 B
*

*>
*

*> LOC.REP.GROUP1 40 40
*

*> 4.38474 128.616 3.51
*

*> 0 P
*

*>
*

*> Variance 192 166
*

*> 1.00000 29.3327 8.09
*

*> 0 P
*

*>
*

*>
*

*>
*

*> 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.
*

*>
*

*>
*

*>
*

*> Analysis of Variance
*

*> NumDF DenDF_con F_inc F_con M
*

*> P_con
*

*>
*

*> 10
*

*> mu
*

*> 1 3.0 2786.24
*

*> 2786.24 . <.001
*

*>
*

*> 5 GROUP1
*

*> 4 28.2 1.48 1.48 A
*

*> 0.235
*

*>
*

*> 11 GROUP1.ENTRY 21
*

*> 131.7 1.06 1.06 B 0.405
*

*>
*

*> Notice: The DenDF values are
*

*> calculated ignoring
*

*> fixed/boundary/singular
*

*>
*

*> variance parameters
*

*> using algebraic derivatives.
*

*>
*

*> 1 LOC
*

*> 4 effects fitted
*

*>
*

*> 12 LOC.REP
*

*> 8 effects fitted
*

*>
*

*> 13 LOC.GROUP1
*

*> 20 effects fitted
*

*>
*

*> 15 LOC.REP.GROUP1
*

*> 40 effects fitted
*

*>
*

*> Finished: 05 Nov 2009 13:52:27.129
*

*> LogL Converged
*

*>
*

*>
*

*> ASReml 2.00b [01 Jul 2006] ASREML
*

*> GUBD MODULE
*

*>
*

*> Build: w [ 1 Oct 2008] 32
*

*> bit
*

*>
*

*> 05 Nov 2009 13:53:00.399 1264.00
*

*> Mbyte Windows
*

*> GUBD_Integrated_Module
*

*>
*

*> Licensed to: Monsanto
*

*>
*

*> ***********************************************************
*

*>
*

*> * SYNTAX change: A/B now means
*

*> A A.B *
*

*>
*

*> * *
*

*>
*

*> * Contact support_at_asreml.co.uk for
*

*> licensing and support *
*

*>
*

*> ***************************************************** ARG *
*

*>
*

*> Approximate stratum
*

*> variance decomposition
*

*>
*

*> Stratum Degrees-Freedom
*

*> Variance Component
*

*> Coefficients
*

*>
*

*> LOC 3.00
*

*> 834.703 18.4 9.1 1.8
*

*> 1.0
*

*>
*

*> LOC.REP 4.02
*

*> 441.324 0.0 9.7 1.9
*

*> 1.0
*

*>
*

*> LOC.REP.GROUP1 27.93
*

*> 496.102 0.0 0.0 3.6
*

*> 1.0
*

*>
*

*> Residual Variance 131.05
*

*> 29.3327 0.0 0.0 0.0
*

*> 1.0
*

*>
*

*>
*

*>
*

*> Source Model terms
*

*> Gamma Component Comp/SE %
*

*> C
*

*>
*

*> LOC 4 4
*

*> 0.771952 22.6434 0.56
*

*> 0 P
*

*>
*

*> LOC.REP 8 8
*

*> 0.606630 17.7941 0.54
*

*> 0 P
*

*>
*

*> LOC.GROUP1 20 20
*

*> 0.535386E-07 0.157043E-05 0.00
*

*> 0 B
*

*>
*

*> LOC.REP.GROUP1 40 40
*

*> 4.38474 128.616 3.51
*

*> 0 P
*

*>
*

*> Variance 192 166
*

*> 1.00000 29.3327 8.09
*

*> 0 P
*

*>
*

*>
*

*>
*

*> 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.
*

*>
*

*>
*

*>
*

*> Analysis of Variance
*

*> NumDF DenDF_con F_inc F_con M
*

*> P_con
*

*>
*

*> 10
*

*> mu
*

*> 1 3.0 2786.24 2786.24 .
*

*> <.001
*

*>
*

*> 5 GROUP1
*

*> 4 28.2 1.48
*

*> 1.48 a 0.235
*

*>
*

*> 8 ENTRY
*

*> 21 131.7 1.06 1.06 A
*

*> 0.405
*

*>
*

*> Notice: The DenDF values are
*

*> calculated ignoring
*

*> fixed/boundary/singular
*

*>
*

*> variance parameters
*

*> using algebraic derivatives.
*

*>
*

*> 1 LOC
*

*> 4 effects fitted
*

*>
*

*> 11 LOC.REP
*

*> 8 effects fitted
*

*>
*

*> 12 LOC.GROUP1
*

*> 20 effects fitted
*

*>
*

*> 14 LOC.REP.GROUP1
*

*> 40 effects fitted
*

*>
*

*> Finished: 05 Nov 2009 13:53:00.477
*

*> LogL Converged
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

*> Best Regards,
*

*>
*

*>
*

*>
*

*> Subash Krishnamurthy
*

*>
*

*> BioStatistician
*

*>
*

*> Monsanto
*

*>
*

*> ADR: 800 North Lindbergh Blvd.
*

*>
*

*> Creve Ceour MO-63376
*

*>
*

*> TEL: 314-694-6364
*

*>
*

*>
*

*>
*

*>
*

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*

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-- 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 http://www.CargoVale.com.au/asreml Travel: Tumut 5-6 Nov (RT & BC) Brisbane Probe 29Nov to 6 Dec Bangladesh Proshikkon 31Dec - 6 FebReceived on Sat Nov 06 2009 - 15:53:10 EST

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