Re: Format of pedigree data in BLUP-analysis

Joao Costa e Silva has found in the forestry context that including such
individuals in the analysis can lead to quite large differences in the
estimates of the additive variance. We standardly apply an extra units
variance with a possible positive or negative variance (sorry, don't know
the R way of doing that) to such analysis to avoid bias in the variance
estimates. Or we exclude them from variance estimation.

I don't know why this happens, but presumably as individuals with no parents
these are treated as unrelated founders in the pedigree and are somehow
given high weight in the variance estimation. They may, in fact, be
related, or they may come from different populations.

Greg Dutkowski

Quantitative Geneticist

PlantPlan Genetics http://www.plantplan.com

c/- School of Plant Science

University of Tasmania

Private Bag 55

HOBART 7001

+61-3-62262213 (w) +61-408-238495 (mob) +61-3-62262698 (fax)

From: ASReml users discussion group [mailto:ASREML-L_at_DPI.NSW.GOV.AU] On
Behalf Of Christof Pietsch
Sent: Tuesday, 13 October 2009 7:41 PM
To: ASREML-L_at_DPI.NSW.GOV.AU
Subject: Format of pedigree data in BLUP-analysis

Dear all,
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.
Thank you very much in advance!
Christof

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Received on Thu Oct 14 2009 - 10:19:34 EST