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

Author

Listed:
  • Lim Johan

    (Seoul National University, Department of Statistics, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea (Republic of))

  • Yu Donghyeon

    (Inha University, Department of Statistics, 100 Inha-ro, Michuhol-gu, Incheon 22212, Korea (Republic of))

  • Kuo Hsun-chih

    (National Kaohsiung University of Science and Technology, Department of Risk Management and Insurance, 2 Jhuoyue Rd., Nanzih, Kaohsiung City, 811, Taiwan)

  • Choi Hyungwon

    (Yong Loo Lin School of Medicine, National University of Singapore, Department of Medicine, 14 Medical Dr 117599, Singapore 117599, Singapore)

  • Walmsley Scott

    (Masonic Cancer Center, University of Minnesota, 2231 6th St. SE Minneapolis, MN 55455, United States of America)

Abstract

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.

Suggested Citation

  • Lim Johan & Yu Donghyeon & Kuo Hsun-chih & Choi Hyungwon & Walmsley Scott, 2019. "Truncated rank correlation (TRC) as a robust measure of test-retest reliability in mass spectrometry data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 18(4), pages 1-25, August.
    • Handle: RePEc:bpj:sagmbi:v:18:y:2019:i:4:p:25:n:3
    DOI: 10.1515/sagmb-2018-0056
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