IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0031505.html
   My bibliography  Save this article

Uniform Approximation Is More Appropriate for Wilcoxon Rank-Sum Test in Gene Set Analysis

Author

Listed:
  • Zhide Fang
  • Ruofei Du
  • Xiangqin Cui

Abstract

Gene set analysis is widely used to facilitate biological interpretations in the analyses of differential expression from high throughput profiling data. Wilcoxon Rank-Sum (WRS) test is one of the commonly used methods in gene set enrichment analysis. It compares the ranks of genes in a gene set against those of genes outside the gene set. This method is easy to implement and it eliminates the dichotomization of genes into significant and non-significant in a competitive hypothesis testing. Due to the large number of genes being examined, it is impractical to calculate the exact null distribution for the WRS test. Therefore, the normal distribution is commonly used as an approximation. However, as we demonstrate in this paper, the normal approximation is problematic when a gene set with relative small number of genes is tested against the large number of genes in the complementary set. In this situation, a uniform approximation is substantially more powerful, more accurate, and less intensive in computation. We demonstrate the advantage of the uniform approximations in Gene Ontology (GO) term analysis using simulations and real data sets.

Suggested Citation

  • Zhide Fang & Ruofei Du & Xiangqin Cui, 2012. "Uniform Approximation Is More Appropriate for Wilcoxon Rank-Sum Test in Gene Set Analysis," PLOS ONE, Public Library of Science, vol. 7(2), pages 1-7, February.
  • Handle: RePEc:plo:pone00:0031505
    DOI: 10.1371/journal.pone.0031505
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031505
    Download Restriction: no

    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0031505&type=printable
    Download Restriction: no

    File URL: https://libkey.io/10.1371/journal.pone.0031505?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
    ---><---

    Citations

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


    Cited by:

    1. Rousseau, Ronald & GarcĂ­a-Zorita, Carlos & Sanz-Casado, Elias, 2013. "The h-bubble," Journal of Informetrics, Elsevier, vol. 7(2), pages 294-300.

    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:plo:pone00:0031505. 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.

    We have no bibliographic references for this item. You can help adding them by using 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: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    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.