Outlier detection methods for generalized lattices: a case study on the transition from ANOVA to REML

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Angela-Maria Bernal-VasquezHans-Peter Piepho

Abstract

We review and propose several methods for identifying possible outliers and evaluate their properties. The methods are applied to a genomic prediction program in hybrid rye. Many plant breeders use ANOVA-based software for routine analysis of field trials. These programs may offer specific in-built options for residual analysis that are lacking in current REML software. With the advance of molecular technologies, there is a need to switch to REML-based approaches, but without losing the good features of outlier detection methods that have proven useful in the past. Our aims were to compare the variance component estimates between ANOVA and REML approaches, to scrutinize the outlier detection method of the ANOVA-based package PlabStat and to propose and evaluate alternative procedures for outlier detection. We compared the outputs produced using ANOVA and REML approaches of four published datasets of generalized lattice designs. Five outlier detection methods are explained step by step. Their performance was evaluated by measuring the true positive rate and the false positive rate in a dataset with artificial outliers simulated in several scenarios. An implementation of genomic prediction using an empirical rye multi-environment...Continue Reading

References

Jul 20, 2007·Biometrical Journal. Biometrische Zeitschrift·Juvêncio Santos Nobre, Julio da Motta Singer
Feb 18, 2011·BMC Medical Research Methodology·Freedom N Gumedze, Dan Jackson
Feb 11, 2015·G3 : Genes - Genomes - Genetics·Marco Lopez-CruzGustavo de los Campos

❮ Previous
Next ❯

Citations

Dec 5, 2018·Scientific Data·Maria Y GonzalezAlbert W Schulthess
Apr 26, 2019·Journal of Experimental Botany·Santiago Alvarez PradoNadine Hilgert
Nov 24, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·K O G DiasM M Pastina
Oct 1, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Ana L Galiano-CarneiroThomas Miedaner
Jun 2, 2017·BMC Genetics·Angela-Maria Bernal-VasquezHans-Peter Piepho
Jul 1, 2018·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Maria Y GonzálezJochen C Reif
Jul 19, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Rodrigo José GalánThomas Miedaner
Feb 26, 2021·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Rodrigo José GalánThomas Miedaner
Oct 12, 2021·Frontiers in Plant Science·Maximilian RembeYusheng Zhao
Nov 23, 2021·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Xintian ZhuTobias Würschum
Dec 18, 2021·Frontiers in Plant Science·Dongdong LiWenxin Liu

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.