Imputing Missing Values in Multi-Environment Trials Using the Singular Value Decomposition: an Empirical Comparison

Authors: Sergio Arciniegas-Alarcón, Marisol García-Peña, Wojtek Krzanowski, Carlos Tadeu dos Santos Dias

Missing values for some genotype-environment combinations are commonly encountered in multienvironment trials. The recommended methodology for analyzing such unbalanced data combines the Expectation-Maximization (EM) algorithm with the additive main effects and multiplicative interaction (AMMI) model. Recently, however, four imputation algorithms based on the Singular Value Decomposition of a matrix (SVD) have been reported in the literature (Biplot imputation, EM+SVD, GabrielEigen imputation, and distribution free multiple imputation - DFMI). These algorithms all fill in the missing values, thereby removing the lack of balance in the original data and permitting simpler standard analyses to be performed. The aim of this paper is to compare these four algorithms with the gold standard EM-AMMI. To do this, we report the results of a simulation study based on three complete sets of real data (eucalyptus, sugar cane and beans) for various imputation percentages. The methodologies were compared using the normalised root mean squared error, the Procrustes similarity statistic and the Spearman correlation coefficient. The conclusion is that imputation using the EM algorithm plus SVD provides competitive results to those obtained with the gold standard. It is also an excellent alternative to imputation with an additive model, which in practice ignores the genotype-by-environment interaction and therefore may not be appropriate in some cases.

Comments: 17 Pages.

Download: PDF

Submission history

[v1] 2014-11-03 07:05:31

Unique-IP document downloads: 183 times is a pre-print repository rather than a journal. Articles hosted may not yet have been verified by peer-review and should be treated as preliminary. In particular, anything that appears to include financial or legal advice or proposed medical treatments should be treated with due caution. will not be responsible for any consequences of actions that result from any form of use of any documents on this website.

Add your own feedback and questions here:
You are equally welcome to be positive or negative about any paper but please be polite. If you are being critical you must mention at least one specific error, otherwise your comment will be deleted as unhelpful.

comments powered by Disqus