Multivariate analysis using a giv file

From: yutao <asremlforum_at_VSNI.CO.UK>
Date: Fri, 16 Jan 2009 00:14:48 +0000

Dear Arthur,
I have the data set which contains the weight measurement from 576 animals (the same sex and similar age) sampled from two environments (each environment has two sites). I do not have pedigree information (i.e. sire or dam of an individual animals), instead I have a calculated relationship matrix (i.e. similarity coefficients between progeny based on the number of common alleles shared across 10 microsatellite markers). From the ASReml manual, I know it is possible to use an inverse relationship matrix (a GIV matrix) to run an animal model.

I have prepared a giv file (ped.giv) which is the inverse of the above mentioned relationship matrix and the .as file shown below. What I aim to do is to calculate genetic correlation of animal weights of two environments (i.e, two environments single trait treated as multivariate). The data file is attached here for your information. Since GIV file is too big to attach here (4MB), I only show the part of data to show how the format is.

The error message I have is: Fault 1 Define structure for giv(animal,1).

Bivariate analysis for 2 environment animals
 environ 2 #pond and raceway
 site 4 !A #4 site 2 ponds and 2 raceways
 sx 1 !A #sex
ffphen1.dat !skip 1 !dopart $A

# use an animal model for environ 1 (480 animals)
!part 1
!filter environ !select 1
weight ~ mu site !r giv(animal,1) 0.25

#use an animal model for environ 2 (96 animals)
!part 2
!filter environ !select 2
weight ~ mu site !r giv(animal,1) 0.25

#Both environs, as single trait but different
#error variance
!part 3
weight ~ mu environ !r environ.animal

#There are two separate errors, with one dimension
2 1 1
#error environ 1
480 0 IDEN !S2=80
96 0 IDEN !S2=65
#environ.animal 2
environ 0 CORR 0.65 15 20

Any comments and help are highly appreciated.

Kind regards

Yutao Li

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Received on Sat Jan 16 2009 - 00:14:48 EST

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