IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0063290.html
   My bibliography  Save this article

Stouffer’s Test in a Large Scale Simultaneous Hypothesis Testing

Author

Listed:
  • Sang Cheol Kim
  • Seul Ji Lee
  • Won Jun Lee
  • Young Na Yum
  • Joo Hwan Kim
  • Soojung Sohn
  • Jeong Hill Park
  • Jeongmi Lee
  • Johan Lim
  • Sung Won Kwon

Abstract

In microarray data analysis, we are often required to combine several dependent partial test results. To overcome this, many suggestions have been made in previous literature; Tippett’s test and Fisher’s omnibus test are most popular. Both tests have known null distributions when the partial tests are independent. However, for dependent tests, their (even, asymptotic) null distributions are unknown and additional numerical procedures are required. In this paper, we revisited Stouffer’s test based on z-scores and showed its advantage over the two aforementioned methods in the analysis of large-scale microarray data. The combined statistic in Stouffer’s test has a normal distribution with mean 0 from the normality of the z-scores. Its variance can be estimated from the scores of genes in the experiment without an additional numerical procedure. We numerically compared the errors of Stouffer’s test and the two p-value based methods, Tippett’s test and Fisher’s omnibus test. We also analyzed our microarray data to find differentially expressed genes by non-genotoxic and genotoxic carcinogen compounds. Both numerical study and the real application showed that Stouffer’s test performed better than Tippett’s method and Fisher’s omnibus method with additional permutation steps.

Suggested Citation

  • Sang Cheol Kim & Seul Ji Lee & Won Jun Lee & Young Na Yum & Joo Hwan Kim & Soojung Sohn & Jeong Hill Park & Jeongmi Lee & Johan Lim & Sung Won Kwon, 2013. "Stouffer’s Test in a Large Scale Simultaneous Hypothesis Testing," PLOS ONE, Public Library of Science, vol. 8(5), pages 1-11, May.
    • Handle: RePEc:plo:pone00:0063290
    DOI: 10.1371/journal.pone.0063290
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0063290
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0063290&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0063290?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
    ---><---

    References listed on IDEAS

    as
    1. Kost, James T. & McDermott, Michael P., 2002. "Combining dependent P-values," Statistics & Probability Letters, Elsevier, vol. 60(2), pages 183-190, November.
    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. Joel Bank & Hamish Fitchett & Adam Gorajek & Benjamin A. Malin & Andrew Staib, 2021. "Online Appendix: Star Wars at Central Banks," Staff Report 621, Federal Reserve Bank of Minneapolis.

    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. Arie Shaus & Yana Gerber & Shira Faigenbaum-Golovin & Barak Sober & Eli Piasetzky & Israel Finkelstein, 2020. "Forensic document examination and algorithmic handwriting analysis of Judahite biblical period inscriptions reveal significant literacy level," PLOS ONE, Public Library of Science, vol. 15(9), pages 1-15, September.
    2. Xiaqiong Wang & Yalu Wen, 2020. "A Systematic Comparison of Methods Designed for Association Analysis with Multi-Omics Data," Biostatistics and Biometrics Open Access Journal, Juniper Publishers Inc., vol. 10(2), pages 30-40, August.
    3. Chien Li-Chu, 2020. "Combining dependent p-values by gamma distributions," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 19(4-6), pages 1-12, December.
    4. Holm, Hakan J. & Samahita, Margaret, 2018. "Curating social image: Experimental evidence on the value of actions and selfies," Journal of Economic Behavior & Organization, Elsevier, vol. 148(C), pages 83-104.
    5. Oliver M. Crook & Colin T. R. Davies & Lisa M. Breckels & Josie A. Christopher & Laurent Gatto & Paul D. W. Kirk & Kathryn S. Lilley, 2022. "Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
    6. Clara Bicalho & Adam Bouyamourn & Thad Dunning, 2022. "Conditional Balance Tests: Increasing Sensitivity and Specificity With Prognostic Covariates," Papers 2205.10478, arXiv.org.
    7. Follmann, Dean & Proschan, Michael, 2012. "A test of location for exchangeable multivariate normal data with unknown correlation," Journal of Multivariate Analysis, Elsevier, vol. 104(1), pages 115-125, February.
    8. Peter M. Aronow, 2012. "A General Method for Detecting Interference Between Units in Randomized Experiments," Sociological Methods & Research, , vol. 41(1), pages 3-16, February.

    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:pone00:0063290. 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: 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.