Dear Yuandan
The lsmeans you have are all mixed up.
See below.
> X-Sender: yzhang@metz.une.edu.au
> Date: Wed, 10 Jun 1998 09:41:58 +1000
> To: asreml@chiswick.anprod.CSIRO.AU
> From: Yuandan Zhang <yzhang@metz.une.edu.au>
> Subject: lsmeans
> Mime-Version: 1.0
>
> Dear asreml users,
> I run a mixed model using asreml to estimate heritibilities for antibody
> measurements. I am interested in least squares means of some fixed effects
> and their interations too. In this model, 2 bloodlines, 3 experiment groups
> and their interactions (six levels) are fitted as fixed effects. But it is
> interesting that three of six lsmeans and stderr for interations are
> exactly the same for all 11 bleedings. obiously there is some thing wrong.
> Can some one diagnosis and explain more about the lsmeans output for me?
> Regards,
>
> Yuandan
> Following are the as, pin, and pvs files of one bleeding for your reference.
>
> ab.as
> Chiswick trial on antibody measurements
> animal !P
> sire
> dam
> pen 90
> line 2 #1 IRH 2 CH
> exptgp 3 #1 control, 2 irridiated larve(low dose),
> #3 normal larve, high dose.
> wwt # covariate
> ab_13_3
> ab.txt !MAXIT 20
> ab.txt !MAXIT 20
> ab_29_5 ~mu line exptgp exptgp.line !r animal
>
> ab.pin
>
> F VarPhen 1 2
> H heritibility 1 3
> e_lmeans {7 8}/2 {9:11}/3 [1:6] 12
> lmeans {1:6}/6 {9:11}/3 [7 8] 12
> exmeans {1:6}/6 {7 8}/2 [9:11] 12
>
The problems with this code are:
1 Columns should be referenced in order [e_lmeans and lmeans do not satisfy
this requirement.
2 You have assumed the wrong order of factors for E and L
You need to check the .asr or .sln file to see what the order is.
The model said mu L E E.L so the order becomes E.L E L mu as below
3 For complex situations, it is helpful to map out each predicted mean.
Then collapse them where that is possible.
>From the model, the effects can be identified as
E1L1 E1L2 E2L1 E2L2 E3L1 E3L2 E1 E2 E3 L1 L2 mu
1 2 3 4 5 6 7 8 9 10 11 12
E1L1 1 7 10 12
E1L2 2 7 11 12
E2L1 3 8 10 12
E2L2 4 8 11 12
E3L1 5 9 10 12
E3L2 6 9 11 12
E1 {1 2}/2 7 {10 11}/2 12
E2 {3 4}/2 8 {10 11}/2 12
E3 {5 6}/2 9 {10 11}/2 12
L1 {1 3 5}/3 {7 8 9}/3 10 12
L2 {2 4 6}/3 {7 8 9}/3 11 12
The first 6 of these lines could be contracted to
E1L [ 1 2 ] 7 // [10 11] 12
E2L [ 3 4 ] 8 // [10 11] 12
E3L [ 5 6 ] 9 // [10 11] 12
but the presense of the interaction prevents the other lines
from being contracted.
If you had used the model mu c(L) c(E) c(E.L)
The coefficients would have been [assuming all six E.L combnations were present)
E1L1 E2L1 E1 E2 L1 mu
1 2 3 4 5 6
and the means would then be predicted by
EL1 [ 1 2 0 ] // [ 3 4 0 ] 5 6
El2 [ 1 2 0 ] *-1 // [ 3 4 0 ] -5 6
E [3 4 0 ] 6
L [5 0] 6
You might like to check this and let me know if it doesn't work.
I believe it should.
<><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
Arthur Gilmour PhD email: Arthur.Gilmour@agric.nsw.gov.au
Senior 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 currently free by anonymous ftp from pub/aar on ftp.res.bbsrc.ac.uk
Point your web browser at ftp://ftp.res.bbsrc.ac.uk/pub/aar/
in the IACR-Rothamsted information system http://www.res.bbsrc.ac.uk/
To join the asreml discussion list, send the message
subscribe
to asreml-request@chiswick.anprod.CSIRO.au
The address for messages to the list is asreml@chiswick.anprod.CSIRO.au
<> <> <> <> <> <> <>
"Seek first the kingdom of God and His righteousness" Jesus; Matthew 6: 33
<><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>