Variable selection for binary classification using error rate p-values applied to metabolomics data

BMC Bioinformatics
Mari van ReenenJ Hendrik Venter

Abstract

Metabolomics datasets are often high-dimensional though only a limited number of variables are expected to be informative given a specific research question. The important task of selecting informative variables can therefore become complex. In this paper we look at discriminating between two groups. Two tasks need to be performed: (i) finding variables which differ between the two groups; and (ii) determining how the selected variables can be used to classify new subjects. We introduce an approach using minimum classification error rates as test statistics to find discriminatory and therefore informative variables. The thresholds resulting in the minimum error rates can be used to classify new subjects. This approach transforms error rates into p-values and is referred to as ERp. We show that non-parametric hypothesis testing, based on minimum classification error rates as test statistics, can find statistically significantly shifted variables. The discriminatory ability of variables becomes more apparent when error rates are evaluated based on their corresponding p-values, as relatively high error rates can still be statistically significant. ERp can handle unequal and small group sizes, as well as account for the cost of mis...Continue Reading

References

Aug 5, 1999·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·S L LeibW Zimmerli
Mar 21, 2003·European Journal of Pediatrics·Ibrahim M KhanUlrich Laaser
Feb 8, 2005·Critical Care : the Official Journal of the Critical Care Forum·Viv BewickJonathan Ball
Sep 16, 2005·Biometrical Journal. Biometrische Zeitschrift·Ronen FlussBenjamin Reiser
Jan 11, 2008·Annual Review of Pharmacology and Toxicology·Rima Kaddurah-DaoukRichard M Weinshilboum
Jan 28, 2010·Analytica Chimica Acta·Rasmus MadsenJohan Trygg
Apr 2, 2013·Metabolomics : Official Journal of the Metabolomic Society·Jianguo XiaDavid S Wishart
Oct 15, 2013·Statistics in Medicine·Jingjing Yin, Lili Tian
May 1, 2012·Computational Statistics & Data Analysis·Chin-Ying LaiEnrique F Schisterman

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Citations

Jul 23, 2013·PloS One·Marc LemanJean-Pierre Martens
Oct 12, 2017·Frontiers in Neuroscience·Shayne MasonRegan Solomons
Jan 21, 2017·Analytical Chemistry·G A Nagana Gowda, Daniel Raftery

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Methods Mentioned

BETA
nuclear magnetic resonance
NMR

Software Mentioned

SPSS
PLS
Matlab
CART
mathrm
DA
ERp

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