IDEAS home Printed from https://ideas.repec.org/a/bla/stanee/v77y2023i3p284-303.html
   My bibliography  Save this article

Discretized skew‐t mixture model for deconvoluting liquid chromatograph mass spectrometry data

Author

Listed:
  • Xuwen Zhu
  • Xiang Zhang

Abstract

In this paper, new statistical algorithms for accurate peak detection in the metabolomic data are proposed. Specifically, liquid chromatograph‐mass spectrometry data are analyzed. The discretized skew‐t mixture model for peak detection is proposed. It shows great flexibility and capability in fitting skewed or heavy‐tailed peaks. The methodology is further extended to cross‐sample peak alignment for identifying the true peaks. A measure of peak credibility is provided through the assessment of misclassification probabilities between two cross‐sample peaks. The proposed algorithms are applied to spike‐in data with promising results.

Suggested Citation

  • Xuwen Zhu & Xiang Zhang, 2023. "Discretized skew‐t mixture model for deconvoluting liquid chromatograph mass spectrometry data," Statistica Neerlandica, Netherlands Society for Statistics and Operations Research, vol. 77(3), pages 284-303, August.
    • Handle: RePEc:bla:stanee:v:77:y:2023:i:3:p:284-303
    DOI: 10.1111/stan.12285
    as

    Download full text from publisher

    File URL: https://doi.org/10.1111/stan.12285
    Download Restriction: no
    File URL: https://libkey.io/10.1111/stan.12285?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Biernacki, Christophe & Celeux, Gilles & Govaert, Gerard, 2003. "Choosing starting values for the EM algorithm for getting the highest likelihood in multivariate Gaussian mixture models," Computational Statistics & Data Analysis, Elsevier, vol. 41(3-4), pages 561-575, January.
    2. Volodymyr Melnykov, 2013. "Finite mixture modelling in mass spectrometry analysis," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 62(4), pages 573-592, August.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Allassonnière, Stéphanie & Chevallier, Juliette, 2021. "A new class of stochastic EM algorithms. Escaping local maxima and handling intractable sampling," Computational Statistics & Data Analysis, Elsevier, vol. 159(C).
    2. Riccardo Rastelli & Michael Fop, 2020. "A stochastic block model for interaction lengths," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 14(2), pages 485-512, June.
    3. Adrian O’Hagan & Arthur White, 2019. "Improved model-based clustering performance using Bayesian initialization averaging," Computational Statistics, Springer, vol. 34(1), pages 201-231, March.
    4. Maria Iannario, 2012. "Preliminary estimators for a mixture model of ordinal data," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 6(3), pages 163-184, October.
    5. Amanda F. Mejia, 2022. "Discussion on “distributional independent component analysis for diverse neuroimaging modalities” by Ben Wu, Subhadip Pal, Jian Kang, and Ying Guo," Biometrics, The International Biometric Society, vol. 78(3), pages 1109-1112, September.
    6. Zhu, Xuwen & Melnykov, Volodymyr, 2018. "Manly transformation in finite mixture modeling," Computational Statistics & Data Analysis, Elsevier, vol. 121(C), pages 190-208.
    7. Lebret, Rémi & Iovleff, Serge & Langrognet, Florent & Biernacki, Christophe & Celeux, Gilles & Govaert, Gérard, 2015. "Rmixmod: The R Package of the Model-Based Unsupervised, Supervised, and Semi-Supervised Classification Mixmod Library," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 67(i06).
    8. Faicel Chamroukhi, 2016. "Piecewise Regression Mixture for Simultaneous Functional Data Clustering and Optimal Segmentation," Journal of Classification, Springer;The Classification Society, vol. 33(3), pages 374-411, October.
    9. Roberto Mari & Salvatore Ingrassia & Antonio Punzo, 2023. "Local and Overall Deviance R-Squared Measures for Mixtures of Generalized Linear Models," Journal of Classification, Springer;The Classification Society, vol. 40(2), pages 233-266, July.
    10. O’Hagan, Adrian & Murphy, Thomas Brendan & Gormley, Isobel Claire, 2012. "Computational aspects of fitting mixture models via the expectation–maximization algorithm," Computational Statistics & Data Analysis, Elsevier, vol. 56(12), pages 3843-3864.
    11. Melnykov, Volodymyr & Melnykov, Igor, 2012. "Initializing the EM algorithm in Gaussian mixture models with an unknown number of components," Computational Statistics & Data Analysis, Elsevier, vol. 56(6), pages 1381-1395.
    12. Melnykov, Volodymyr, 2016. "ClickClust: An R Package for Model-Based Clustering of Categorical Sequences," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 74(i09).
    13. Schücking, Maximilian & Jochem, Patrick, 2021. "Two-stage stochastic program optimizing the cost of electric vehicles in commercial fleets," Applied Energy, Elsevier, vol. 293(C).
    14. Fabian Dvorak, 2020. "stratEst: Strategy Estimation in R," TWI Research Paper Series 119, Thurgauer Wirtschaftsinstitut, Universität Konstanz.
    15. Di Mari, Roberto & Bakk, Zsuzsa & Oser, Jennifer & Kuha, Jouni, 2023. "A two-step estimator for multilevel latent class analysis with covariates," LSE Research Online Documents on Economics 119994, London School of Economics and Political Science, LSE Library.
    16. Reddy, Chandan K. & Rajaratnam, Bala, 2010. "Learning mixture models via component-wise parameter smoothing," Computational Statistics & Data Analysis, Elsevier, vol. 54(3), pages 732-749, March.
    17. Francesco Lagona & Antonello Maruotti & Fabio Padovano, 2015. "Multilevel multivariate modelling of legislative count data, with a hidden Markov chain," Journal of the Royal Statistical Society Series A, Royal Statistical Society, vol. 178(3), pages 705-723, June.
    18. You, Na & Dai, Hongsheng & Wang, Xueqin & Yu, Qingyun, 2024. "Sequential estimation for mixture of regression models for heterogeneous population," Computational Statistics & Data Analysis, Elsevier, vol. 194(C).
    19. repec:jss:jstsof:46:i06 is not listed on IDEAS
    20. Semhar Michael & Volodymyr Melnykov, 2016. "An effective strategy for initializing the EM algorithm in finite mixture models," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 10(4), pages 563-583, December.
    21. Melnykov, Volodymyr & Zhu, Xuwen, 2018. "On model-based clustering of skewed matrix data," Journal of Multivariate Analysis, Elsevier, vol. 167(C), pages 181-194.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:bla:stanee:v:77:y:2023:i:3:p:284-303. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Wiley Content Delivery (email available below). General contact details of provider: http://www.blackwellpublishing.com/journal.asp?ref=0039-0402 .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.