Re: Contrasts in ASREML

From: <arthur.gilmour_at_DPI.NSW.GOV.AU>
Date: Tue, 7 Nov 2006 15:42:53 +1100

Dear Brian,

Thanks for your enquiry:
You wrote:

Hi, I noticed that in Version 2 there is a section on running contrasts (page 62 of the manual).

Can someone explain (maybe with an example) of how to specify the contrast
in more detail? Do we actually put the new defined contrast term in the
model (LinN in the manual's example)? Which file are the results of the contrast(s) output to? Thanks in advance, bb

The test example is a variation on the Oats example (Section 15.2 in the
User Guide)
for which you should have the data.

!WORK 150 !EPS !ARG 1
   !DOPART $1
Split plot analysis - oat Variety.Nitrogen
# "C:\new.txt (Created by Genstat: 13:54:37 06/01/99)"
# blocks nitrogen subplots variety wplots yield
# 1 0.6_cwt 1 Marvellous 1 156
# 1 0.4_cwt 2 Marvellous 1 118
# 1 0.2_cwt 3 Marvellous 1 140
# 1 0_cwt 4 Marvellous 1 105
# 1 0_cwt 1 Victory 2 111
# 1 0.2_cwt 2 Victory 2 130
# 1 0.6_cwt 3 Victory 2 174
# 1 0.4_cwt 4 Victory 2 157
 blocks *
 nitrogen !A
 variety !A
 wplots *
oats.asd !skip 1 !FCON
!CONTRAST LinNitr nitrogen .6 .4 .2 0


yield ~ mu,
 LinN c(variety) c(nitrogen) ,
 LinN.c(variety) c(variety).c(nitrogen),
 !r blocks blocks.wplots

The CONtrast mechanism is basically equivalent to creating a new variable
in the data
by adding to the definition part

 LinNitr !=nitrogen !set 0.6 0.4 0.2 0.0

except that that using a transformation means that ASReml does not
know that LinNitr has a one to one relationship with 'nitrogen
so would do the wrong thing with

predict nitrogen

Using a !CONTRAST means ASReml knows the one on one relationship
and so does the right thing with

predict nitrogen

Otherwise, these approaches are equivalent
so fitting mu LinNitr nitrogen
will generate 1 1 2 degrees of freedom respectively
and the F tests will be
nitrogen ! mu, LinNitr

I hope that gives a few more clues.

Grace, mercy and peace to you from God our Saviour Jesus Christ

Arthur Gilmour PhD
Principal Research Scientist (Biometrics)
NSW Department of Primary Industries
Orange Agricultural Institute, Forest Rd, ORANGE, 2800, AUSTRALIA

fax: 02 6391 3899; 02 6391 3922 Australia +61
telephone work: 02 6391 3815; home: 02 6364 3288; mobile: 0438 251 426
Personal website:

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Received on Sun Nov 07 2006 - 15:42:53 EST

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