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Statistical Applications in Genetics and Molecular Biology

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Volume 18, Issue 4


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Truncated rank correlation (TRC) as a robust measure of test-retest reliability in mass spectrometry data

Johan Lim
  • Seoul National University, Department of Statistics, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea (Republic of)
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/ Donghyeon Yu
  • Corresponding author
  • Inha University, Department of Statistics, 100 Inha-ro, Michuhol-gu, Incheon 22212, Korea (Republic of)
  • Email
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/ Hsun-chih Kuo
  • National Kaohsiung University of Science and Technology, Department of Risk Management and Insurance, 2 Jhuoyue Rd., Nanzih, Kaohsiung City, 811, Taiwan
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/ Hyungwon Choi
  • Yong Loo Lin School of Medicine, National University of Singapore, Department of Medicine, 14 Medical Dr 117599, Singapore 117599, Singapore
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/ Scott Walmsley
  • Masonic Cancer Center, University of Minnesota, 2231 6th St. SE Minneapolis, MN 55455, United States of America
  • University of Colorado Anschutz Medical Campus, 13001 E 17th Pl, Aurora, CO 80045, United States of America
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Published Online: 2019-05-30 | DOI: https://doi.org/10.1515/sagmb-2018-0056


In mass spectrometry (MS) experiments, more than thousands of peaks are detected in the space of mass-to-charge ratio and chromatographic retention time, each associated with an abundance measurement. However, a large proportion of the peaks consists of experimental noise and low abundance compounds are typically masked by noise peaks, compromising the quality of the data. In this paper, we propose a new measure of similarity between a pair of MS experiments, called truncated rank correlation (TRC). To provide a robust metric of similarity in noisy high-dimensional data, TRC uses truncated top ranks (or top m-ranks) for calculating correlation. A comprehensive numerical study suggests that TRC outperforms traditional sample correlation and Kendall’s τ. We apply TRC to measuring test-retest reliability of two MS experiments, including biological replicate analysis of the metabolome in HEK293 cells and metabolomic profiling of benign prostate hyperplasia (BPH) patients. An R package trc of the proposed TRC and related functions is available at https://sites.google.com/site/dhyeonyu/software.

Keywords: Kendall’s τ; mass spectrometry data; test-retest reliability; truncated rank


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About the article

Published Online: 2019-05-30

Funding Source: National Research Foundation of Korea

Award identifier / Grant number: NRF-2018R1C1B6001108

National Research Foundation of Korea, Funder Id: http://dx.doi.org/10.13039/501100003725, Grant Number: NRF-2018R1C1B6001108.

Citation Information: Statistical Applications in Genetics and Molecular Biology, Volume 18, Issue 4, 20180056, ISSN (Online) 1544-6115, DOI: https://doi.org/10.1515/sagmb-2018-0056.

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