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https://hdl.handle.net/1959.11/3682
Title: | Perils of Parsimony: Properties of Reduced-Rank Estimates of Genetic Covariance Matrices | Contributor(s): | Meyer, Karin (author); Kirkpatrick, Mark (author) | Publication Date: | 2008 | DOI: | 10.1534/genetics.108.090159 | Handle Link: | https://hdl.handle.net/1959.11/3682 | Abstract: | Eigenvalues and eigenvectors of covariance matrices are important statistics for multivariate problems in many applications, including quantitative genetics. Estimates of these quantities are subject to different types of bias. This article reviews and extends the existing theory on these biases, considering a balanced one-way classification and restricted maximum-likelihood estimation. Biases are due to the spread of sample roots and arise from ignoring selected principal components when imposing constraints on the parameter space, to ensure positive semidefinite estimates or to estimate covariance matrices of chosen, reduced rank. In addition, it is shown that reduced-rank estimators that consider only the leading eigenvalues and -vectors of the 'between-group' covariance matrix may be biased due to selecting the wrong subset of principal components. In a genetic context, with groups representing families, this bias is inverse proportional to the degree of genetic relationship among family members, but is independent of sample size. Theoretical results are supplemented by a simulation study, demonstrating close agreement between predicted and observed bias for large samples. It is emphasized that the rank of the genetic covariance matrix should be chosen sufficiently large to accommodate all important genetic principal components, even though, paradoxically, this may require including a number of components with negligible eigenvalues. A strategy for rank selection in practical analyses is outlined. | Publication Type: | Journal Article | Source of Publication: | Genetics, 180(2), p. 1153-1166 | Publisher: | Genetics Society of America | Place of Publication: | United States of America | ISSN: | 1943-2631 0016-6731 |
Fields of Research (FoR) 2008: | 060412 Quantitative Genetics (incl Disease and Trait Mapping Genetics) | Socio-Economic Objective (SEO) 2008: | 830301 Beef Cattle | Peer Reviewed: | Yes | HERDC Category Description: | C1 Refereed Article in a Scholarly Journal |
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Appears in Collections: | Animal Genetics and Breeding Unit (AGBU) Journal Article |
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