IDEAS home Printed from https://ideas.repec.org/a/eee/csdana/v52y2008i8p4104-4115.html
   My bibliography  Save this article

New normalization methods using support vector machine quantile regression approach in microarray analysis

Author

Listed:
  • Sohn, Insuk
  • Kim, Sujong
  • Hwang, Changha
  • Lee, Jae Won

Abstract

There are many sources of systematic variations in cDNA microarray experiments which affect the measured gene expression levels. Print-tip lowess normalization is widely used in situations where dye biases can depend on spot overall intensity and/or spatial location within the array. However, print-tip lowess normalization performs poorly in situations where error variability for each gene is heterogeneous over intensity ranges. We first develop support vector machine quantile regression (SVMQR) by extending support vector machine regression (SVMR) for the estimation of linear and nonlinear quantile regressions, and then propose some new print-tip normalization methods based on SVMR and SVMQR. We apply our proposed normalization methods to previous cDNA microarray data of apolipoprotein AI-knockout (apoAI-KO) mice, diet-induced obese mice, and genistein-fed obese mice. From our comparative analyses, we find that our proposed methods perform better than the existing print-tip lowess normalization method.

Suggested Citation

  • Sohn, Insuk & Kim, Sujong & Hwang, Changha & Lee, Jae Won, 2008. "New normalization methods using support vector machine quantile regression approach in microarray analysis," Computational Statistics & Data Analysis, Elsevier, vol. 52(8), pages 4104-4115, April.
    • Handle: RePEc:eee:csdana:v:52:y:2008:i:8:p:4104-4115
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0167-9473(08)00053-4
    Download Restriction: Full text for ScienceDirect subscribers only.
    ---><---

    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. Koenker, Roger W & Bassett, Gilbert, Jr, 1978. "Regression Quantiles," Econometrica, Econometric Society, vol. 46(1), pages 33-50, January.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Allison, David B. & Visscher, Peter M. & Rosa, Guilherme J.M. & Amos, Christopher I., 2009. "Statistical genetics & statistical genomics: Where biology, epistemology, statistics, and computation collide," Computational Statistics & Data Analysis, Elsevier, vol. 53(5), pages 1531-1534, March.
    2. Hu, Jianming & Tang, Jingwei & Lin, Yingying, 2020. "A novel wind power probabilistic forecasting approach based on joint quantile regression and multi-objective optimization," Renewable Energy, Elsevier, vol. 149(C), pages 141-164.
    3. Songfeng Zheng, 2014. "A generalized Newton algorithm for quantile regression models," Computational Statistics, Springer, vol. 29(6), pages 1403-1426, December.
    4. Edler, Lutz & Lee, Jae Won & Mittlböck, Martina & Niland, Joyce & Victor, Norbert, 2009. "Computational statistics within clinical research," Computational Statistics & Data Analysis, Elsevier, vol. 53(3), pages 583-585, January.

    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. Akosah, Nana Kwame & Alagidede, Imhotep Paul & Schaling, Eric, 2020. "Testing for asymmetry in monetary policy rule for small-open developing economies: Multiscale Bayesian quantile evidence from Ghana," The Journal of Economic Asymmetries, Elsevier, vol. 22(C).
    2. Paul Hewson & Keming Yu, 2008. "Quantile regression for binary performance indicators," Applied Stochastic Models in Business and Industry, John Wiley & Sons, vol. 24(5), pages 401-418, September.
    3. Salimata Sissoko, 2011. "Working Paper 03-11 - Niveau de décentralisation de la négociation et structure des salaires," Working Papers 1103, Federal Planning Bureau, Belgium.
    4. Korom, Philipp, 2016. "Inherited advantage: The importance of inheritance for private wealth accumulation in Europe," MPIfG Discussion Paper 16/11, Max Planck Institute for the Study of Societies.
    5. Daniele, Vittorio, 2007. "Criminalità e investimenti esteri. Un’analisi per le province italiane [The effect of organized crime on Foreign Investments. An Empirical Analysis for the Italian Provinces]," MPRA Paper 6417, University Library of Munich, Germany.
    6. Ma, Lingjie & Koenker, Roger, 2006. "Quantile regression methods for recursive structural equation models," Journal of Econometrics, Elsevier, vol. 134(2), pages 471-506, October.
    7. Dutta, Anupam & Bouri, Elie & Rothovius, Timo & Uddin, Gazi Salah, 2023. "Climate risk and green investments: New evidence," Energy, Elsevier, vol. 265(C).
    8. Cowling, Marc & Ughetto, Elisa & Lee, Neil, 2018. "The innovation debt penalty: Cost of debt, loan default, and the effects of a public loan guarantee on high-tech firms," Technological Forecasting and Social Change, Elsevier, vol. 127(C), pages 166-176.
    9. Haddou, Samira, 2024. "Determinants of CDS in core and peripheral European countries: A comparative study during crisis and calm periods," The North American Journal of Economics and Finance, Elsevier, vol. 71(C).
    10. Niematallah Elamin & Mototsugu Fukushige, 2016. "A Quantile Regression Model for Electricity Peak Demand Forecasting: An Approach to Avoiding Power Blackouts," Discussion Papers in Economics and Business 16-22, Osaka University, Graduate School of Economics.
    11. Peracchi, Franco, 2002. "On estimating conditional quantiles and distribution functions," Computational Statistics & Data Analysis, Elsevier, vol. 38(4), pages 433-447, February.
    12. Jan Fałkowski & Maciej Jakubowski & Paweł Strawiński, 2014. "Returns from income strategies in rural Poland," The Economics of Transition, The European Bank for Reconstruction and Development, vol. 22(1), pages 139-178, January.
    13. Elena Bárcena-Mart�n & Santiago Budr�a & Ana I. Moro-Egido, 2012. "Skill mismatches and wages among European university graduates," Applied Economics Letters, Taylor & Francis Journals, vol. 19(15), pages 1471-1475, October.
    14. Trojanek, Radoslaw & Huderek-Glapska, Sonia, 2018. "Measuring the noise cost of aviation – The association between the Limited Use Area around Warsaw Chopin Airport and property values," Journal of Air Transport Management, Elsevier, vol. 67(C), pages 103-114.
    15. Charlier, Isabelle & Paindaveine, Davy & Saracco, Jérôme, 2015. "Conditional quantile estimation based on optimal quantization: From theory to practice," Computational Statistics & Data Analysis, Elsevier, vol. 91(C), pages 20-39.
    16. Kato, Kengo & F. Galvao, Antonio & Montes-Rojas, Gabriel V., 2012. "Asymptotics for panel quantile regression models with individual effects," Journal of Econometrics, Elsevier, vol. 170(1), pages 76-91.
    17. Ron Diris, 2017. "Don't Hold Back? The Effect of Grade Retention on Student Achievement," Education Finance and Policy, MIT Press, vol. 12(3), pages 312-341, Summer.
    18. Huong Thu Le & Ha Trong Nguyen, 2018. "The evolution of the gender test score gap through seventh grade: new insights from Australia using unconditional quantile regression and decomposition," IZA Journal of Labor Economics, Springer;Forschungsinstitut zur Zukunft der Arbeit GmbH (IZA), vol. 7(1), pages 1-42, December.
    19. Pradeepta Sethi & Brajesh Kumar, 2014. "Financial structure gap and economic development in India," Journal of Business Economics and Management, Taylor & Francis Journals, vol. 15(4), pages 776-794, September.
    20. Paulo M.M. Rodrigues & Rita Fradique Lourenço, 2015. "House prices: bubbles, exuberance or something else? Evidence from euro area countries," Working Papers w201517, Banco de Portugal, Economics and Research Department.

    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:eee:csdana:v:52:y:2008:i:8:p:4104-4115. 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: Catherine Liu (email available below). General contact details of provider: http://www.elsevier.com/locate/csda .

    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.