Estimation of prediction error variances via Monte Carlo sampling methods using different formulations of the prediction error variance.docVIP

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Estimation of prediction error variances via Monte Carlo sampling methods using different formulations of the prediction error variance.doc

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Genetics Selection Evolution BioMedCentral Research Open Access Estimation of prediction error variances via Monte Carlo sampling methods using different formulations of the prediction error variance John M Hickey*1,2,3, Roel F Veerkamp1, Mario PL Calus1, Han A Mulder1 and Robin Thompson4,5,6 Address: 1Animal Breeding and Genomics Centre, Animal Sciences Group, PO Box 65, 8200 AB, Lelystad, The Netherlands, 2Grange Beef Research Centre, Teagasc, Dunsany, Co. Meath, Ireland, 3School of Agriculture, Food and Veterinary Medicine, College of Life Sciences, University College Dublin, Belfield, Dublin 4, Ireland, 4School of Mathematical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK, 5Centre for Mathematical and Computational Biology, Rothamsted Research, Harpenden AL5 2JQ, UK and 6Department of Biomathematics and Bioinformatics, Rothamsted Research, Harpenden AL5 2JQ, UK Email: John M Hickey* - john.hickey@.au; Roel F Veerkamp - roel.veerkamp@wur.nl; Mario PL Calus - mario.calus@wur.nl; Han A Mulder - herman.mulder@wur.nl; Robin Thompson - robin.thompson@bbsrc.ac.uk * Corresponding author Published: 9 February 2009 Received: 17 December 2008 Accepted: 9 February 2009 Genetics Selection Evolution 2009, 41:23 doi:10.1186/1297-9686-41-23 This article is available from: /content/41/1/23 ? 2009 Hickey et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Calculation of the exact prediction error variance covariance matrix is often computationally too demanding, which limits its application in REML algorithms, the calculation of accuracies of estimated breeding values and the control of variance of response to selection. Alternatively Monte Carlo sampling can be used to calcul