IDEAS home Printed from https://ideas.repec.org/a/bpj/sagmbi/v8y2009i1n41.html
   My bibliography  Save this article

M-quantile Regression Analysis of Temporal Gene Expression Data

Author

Listed:
  • Vinciotti Veronica

    (Brunei University)

  • Yu Keming

    (Brunei University)

Abstract

In this paper, we explore the use of M-quantile regression and M-quantile coefficients to detect statistical differences between temporal curves that belong to different experimental conditions. In particular, we consider the application of temporal gene expression data. Here, the aim is to detect genes whose temporal expression is significantly different across a number of biological conditions. We present a new method to approach this problem. Firstly, the temporal profiles of the genes are modelled by a parametric M-quantile regression model. This model is particularly appealing to small-sample gene expression data, as it is very robust against outliers and it does not make any assumption on the error distribution. Secondly, we further increase the robustness of the method by summarising the M-quantile regression models for a large range of quantile values into an M-quantile coefficient. Finally, we fit a polynomial M-quantile regression model to the M-quantile coefficients over time and employ a Hotelling T2-test to detect significant differences of the temporal M-quantile coefficients profiles across conditions. Extensive simulations show the increased power and robustness of M-quantile regression methods over standard regression methods and over some of the previously published methods. We conclude by applying the method to detect differentially expressed genes from time-course microarray data on muscular dystrophy.

Suggested Citation

  • Vinciotti Veronica & Yu Keming, 2009. "M-quantile Regression Analysis of Temporal Gene Expression Data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-22, September.
    • Handle: RePEc:bpj:sagmbi:v:8:y:2009:i:1:n:41
    DOI: 10.2202/1544-6115.1452
    as

    Download full text from publisher

    File URL: https://doi.org/10.2202/1544-6115.1452
    Download Restriction: For access to full text, subscription to the journal or payment for the individual article is required.
    File URL: https://libkey.io/10.2202/1544-6115.1452?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
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Angelini Claudia & De Canditiis Daniela & Mutarelli Margherita & Pensky Marianna, 2007. "A Bayesian Approach to Estimation and Testing in Time-course Microarray Experiments," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 6(1), pages 1-33, September.
    2. Ma, Ping & Zhong, Wenxuan, 2008. "Penalized Clustering of Large-Scale Functional Data With Multiple Covariates," Journal of the American Statistical Association, American Statistical Association, vol. 103, pages 625-636, June.
    3. Ray Chambers & Nikos Tzavidis, 2006. "M-quantile models for small area estimation," Biometrika, Biometrika Trust, vol. 93(2), pages 255-268, June.
    4. Wang, Huixia & He, Xuming, 2007. "Detecting Differential Expressions in GeneChip Microarray Studies: A Quantile Approach," Journal of the American Statistical Association, American Statistical Association, vol. 102, pages 104-112, March.
    5. Yuan, Ming & Kendziorski, Christina, 2006. "Hidden Markov Models for Microarray Time Course Data in Multiple Biological Conditions," Journal of the American Statistical Association, American Statistical Association, vol. 101, pages 1323-1332, December.
    6. Huixia Wang & Xuming He, 2008. "An Enhanced Quantile Approach for Assessing Differential Gene Expressions," Biometrics, The International Biometric Society, vol. 64(2), pages 449-457, June.
    7. Giloni, Avi & Simonoff, Jeffrey S. & Sengupta, Bhaskar, 2006. "Robust weighted LAD regression," Computational Statistics & Data Analysis, Elsevier, vol. 50(11), pages 3124-3140, July.
    8. Kokic, Philip, et al, 1997. "A Measure of Production Performance," Journal of Business & Economic Statistics, American Statistical Association, vol. 15(4), pages 445-451, October.
    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. N. Salvati & N. Tzavidis & M. Pratesi & R. Chambers, 2012. "Small area estimation via M-quantile geographically weighted regression," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 21(1), pages 1-28, March.
    2. Giulia Romano & Nicola Salvati & Andrea Guerrini, 2014. "Factors Affecting Water Utility Companies’ Decision to Promote the Reduction of Household Water Consumption," Water Resources Management: An International Journal, Published for the European Water Resources Association (EWRA), Springer;European Water Resources Association (EWRA), vol. 28(15), pages 5491-5505, December.
    3. Merlo, Luca & Petrella, Lea & Salvati, Nicola & Tzavidis, Nikos, 2022. "Marginal M-quantile regression for multivariate dependent data," Computational Statistics & Data Analysis, Elsevier, vol. 173(C).
    4. Stefano Marchetti & Caterina Giusti & Nicola Salvati & Monica Pratesi, 2017. "Small area estimation based on M-quantile models in presence of outliers in auxiliary variables," Statistical Methods & Applications, Springer;Società Italiana di Statistica, vol. 26(4), pages 531-555, November.
    5. Farcomeni Alessio & Arima Serena, 2012. "A Bayesian autoregressive three-state hidden Markov model for identifying switching monotonic regimes in Microarray time course data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(4), pages 1-31, June.
    6. Marchetti, Stefano & Tzavidis, Nikos & Pratesi, Monica, 2012. "Non-parametric bootstrap mean squared error estimation for M-quantile estimators of small area averages, quantiles and poverty indicators," Computational Statistics & Data Analysis, Elsevier, vol. 56(10), pages 2889-2902.
    7. Otto-Sobotka, Fabian & Salvati, Nicola & Ranalli, Maria Giovanna & Kneib, Thomas, 2019. "Adaptive semiparametric M-quantile regression," Econometrics and Statistics, Elsevier, vol. 11(C), pages 116-129.
    8. Galina Besstremyannaya & Sergei Golovan, 2023. "Measuring heterogeneity in hospital productivity: a quantile regression approach," Journal of Productivity Analysis, Springer, vol. 59(1), pages 15-43, February.
    9. Li, Pai-Ling & Chiou, Jeng-Min, 2011. "Identifying cluster number for subspace projected functional data clustering," Computational Statistics & Data Analysis, Elsevier, vol. 55(6), pages 2090-2103, June.
    10. J. N. K. Rao, 2015. "Inferential issues in model-based small area estimation: some new developments," Statistics in Transition new series, Główny Urząd Statystyczny (Polska), vol. 16(4), pages 491-510, December.
    11. Angelini, Claudia & De Canditiis, Daniela & Pensky, Marianna, 2009. "Bayesian models for two-sample time-course microarray experiments," Computational Statistics & Data Analysis, Elsevier, vol. 53(5), pages 1547-1565, March.
    12. Stefano Marchetti & Luca Secondi, 2017. "Estimates of Household Consumption Expenditure at Provincial Level in Italy by Using Small Area Estimation Methods: “Real” Comparisons Using Purchasing Power Parities," Social Indicators Research: An International and Interdisciplinary Journal for Quality-of-Life Measurement, Springer, vol. 131(1), pages 215-234, March.
    13. G. Bertarelli & R. Chambers & N. Salvati, 2021. "Outlier robust small domain estimation via bias correction and robust bootstrapping," Statistical Methods & Applications, Springer;Società Italiana di Statistica, vol. 30(1), pages 331-357, March.
    14. Marilena Furno, 2010. "A robust test of specification based on order statistics," Computational Statistics, Springer, vol. 25(4), pages 707-723, December.
    15. Cheng, Tsung-Chi, 2012. "On simultaneously identifying outliers and heteroscedasticity without specific form," Computational Statistics & Data Analysis, Elsevier, vol. 56(7), pages 2258-2272.
    16. Valéry Dongmo Jiongo & Pierre Nguimkeu, 2018. "Bootstrapping Mean Squared Errors of Robust Small-Area Estimators: Application to the Method-of-Payments Data," Staff Working Papers 18-28, Bank of Canada.
    17. Breckling, Jens & Kokic, Philip & Lübke, Oliver, 2001. "A note on multivariate M-quantiles," Statistics & Probability Letters, Elsevier, vol. 55(1), pages 39-44, November.
    18. Sungwan Bang & Soo-Heang Eo & Yong Mee Cho & Myoungshic Jhun & HyungJun Cho, 2016. "Non-crossing weighted kernel quantile regression with right censored data," Lifetime Data Analysis: An International Journal Devoted to Statistical Methods and Applications for Time-to-Event Data, Springer, vol. 22(1), pages 100-121, January.
    19. Beibei Zhang & Rong Chen, 2018. "Nonlinear Time Series Clustering Based on Kolmogorov-Smirnov 2D Statistic," Journal of Classification, Springer;The Classification Society, vol. 35(3), pages 394-421, October.
    20. Fabrizi, Enrico & Salvati, Nicola & Trivisano, Carlo, 2020. "Robust Bayesian small area estimation based on quantile regression," Computational Statistics & Data Analysis, Elsevier, vol. 145(C).

    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:bpj:sagmbi:v:8:y:2009:i:1:n:41. 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: Peter Golla (email available below). General contact details of provider: https://www.degruyter.com .

    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.