From: KRISHNAMURTHY, SUBASH [AG/1000] <subash.krishnamurthy_at_MONSANTO.COM>

Date: Thu, 5 Nov 2009 14:03:54 -0600

Date: Thu, 5 Nov 2009 14:03:54 -0600

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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Received on Fri Nov 05 2009 - 14:03:54 EST

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