IDEAS home Printed from https://ideas.repec.org/a/eee/csdana/v53y2009i7p2446-2452.html
   My bibliography  Save this article

How accurate are the extremely small P-values used in genomic research: An evaluation of numerical libraries

Author

Listed:
  • Santosh Bangalore, Sai
  • Wang, Jelai
  • Allison, David B.

Abstract

In the fields of genomics and high-dimensional biology (HDB), massive multiple testing prompts the use of extremely small significance levels. Because tail areas of statistical distributions are needed for hypothesis testing, the accuracy of these areas is important to confidently make scientific judgments. Previous work on accuracy was primarily focused on evaluating professionally written statistical software, like SAS, on the Statistical Reference Datasets (StRD) provided by the National Institute of Standards and Technology (NIST) and on the accuracy of tail areas in statistical distributions. The goal of this paper is to provide guidance to investigators, who are developing their own custom scientific software built upon numerical libraries written by others. Specifically, we evaluate the accuracy of small tail areas from cumulative distribution functions (CDF) of the Chi-square and t-distribution by comparing several open-source, free, or commercially licensed numerical libraries in Java, C, and R to widely accepted standards of comparison like ELV and DCDFLIB. In our evaluation, the C libraries and R functions are consistently accurate up to six significant digits. Amongst the evaluated Java libraries, Colt is the most accurate. These languages and libraries are popular choices among programmers developing scientific software, so the results herein can be useful to programmers in choosing libraries for CDF accuracy.

Suggested Citation

  • Santosh Bangalore, Sai & Wang, Jelai & Allison, David B., 2009. "How accurate are the extremely small P-values used in genomic research: An evaluation of numerical libraries," Computational Statistics & Data Analysis, Elsevier, vol. 53(7), pages 2446-2452, May.
  • Handle: RePEc:eee:csdana:v:53:y:2009:i:7:p:2446-2452
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0167-9473(08)00550-1
    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. Knusel, Leo, 2005. "On the accuracy of statistical distributions in Microsoft Excel 2003," Computational Statistics & Data Analysis, Elsevier, vol. 48(3), pages 445-449, March.
    2. Keeling, Kellie B. & Pavur, Robert J., 2007. "A comparative study of the reliability of nine statistical software packages," Computational Statistics & Data Analysis, Elsevier, vol. 51(8), pages 3811-3831, May.
    3. Altman, Micah & Gill, Jeff & McDonald, Michael P., 2007. "accuracy: Tools for Accurate and Reliable Statistical Computing," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 21(i01).
    Full references (including those not matched with items on IDEAS)

    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:53:y:2009:i:7:p:2446-2452. 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: (Haili He). 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.