Re: Format of pedigree data in BLUP-analysis

From: <brian.cullis_at_INDUSTRY.NSW.GOV.AU>
Date: Wed, 14 Oct 2009 08:18:44 +1100

Dear Christof
I'd like to know, if entries with no pedigree information but with
phenotypes have to be incorporated in the pedigree-data for the
calculation of the numerator relationship matrix in a BLUP-analysis using
the VPEDIGREE-directive.
This is an open question and is difficult to answer in general. I usually
include all entries in the pedigree file if they occur in the data set but
do so with a knowledge of the implications. If there are a large number of
these then you may be better to take an approach similar to that used in
Oakey et al (2007) and (2006) in Theoretical and Applied Genetics. It is
best to consider the application. From a programming viewpoint, the answer
is yes, otherwise there will be a mismatch of levels in the factors I
(I havent checked this recently)

warm regards

Brian Cullis|Research Leader, Biometrics &
Senior Principal Research Scientist |
Industry & Investment NSW | Wagga Wagga Agricultural Institute | Pine
Gully Road | Wagga Wagga NSW 2650 |
PMB | Wagga Wagga NSW 2650
T: 02 6938 1855 | M: 0439 448 591 | F: 02 6938 1809 | E:,au
W: |

Visiting Professorial Fellow
School of Mathematics and Applied Statistics
Faculty of Informatics
University of Wollongong

Faculty of Agriculture, Food & Natural Resources
The University of Sydney

Adjunct Professor
School of Computing and Mathematics
Charles Sturt University
Received on Thu Oct 14 2009 - 08:18:44 EST

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