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. Songfeng Zheng, 2014. "A generalized Newton algorithm for quantile regression models," Computational Statistics, Springer, vol. 29(6), pages 1403-1426, December.
    3. 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.

    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.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: (Dana Niculescu). General contact details of provider: http://www.elsevier.com/locate/csda .

    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 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.

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

    IDEAS is a RePEc service hosted by the Research Division of the Federal Reserve Bank of St. Louis . RePEc uses bibliographic data supplied by the respective publishers.