IDEAS home Printed from https://ideas.repec.org/a/bpj/sagmbi/v8y2009i1n7.html
   My bibliography  Save this article

A Multiple Testing Approach to High-Dimensional Association Studies with an Application to the Detection of Associations between Risk Factors of Heart Disease and Genetic Polymorphisms

Author

Listed:
  • Ferreira José A.

    (Vrije University Medical Center)

  • Berkhof Johannes

    (Vrije University Medical Center)

  • Souverein Olga

    (Wageningen University)

  • Zwinderman Koos

    (University of Amsterdam)

Abstract

We present an approach to association studies involving a dozen or so `response' variables and a few hundred `explanatory' variables which emphasizes transparency, simplicity, and protection against spurious results. The methods proposed are largely non-parametric, and they are systematically rounded-off by the Benjamini-Hochberg method of multiple testing. An application to the detection of associations between risk factors of heart disease and genetic polymorphisms using the REGRESS dataset provides ample illustration of our approach. Special attention is paid to book-keeping and information-management aspects of data analysis, which allow the creation of an informative and reasonably digestible `map of relationships'---the end-product of an association study as far as statistics is concerned.

Suggested Citation

  • Ferreira José A. & Berkhof Johannes & Souverein Olga & Zwinderman Koos, 2009. "A Multiple Testing Approach to High-Dimensional Association Studies with an Application to the Detection of Associations between Risk Factors of Heart Disease and Genetic Polymorphisms," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-58, January.
    • Handle: RePEc:bpj:sagmbi:v:8:y:2009:i:1:n:7
    DOI: 10.2202/1544-6115.1420
    as

    Download full text from publisher

    File URL: https://doi.org/10.2202/1544-6115.1420
    Download Restriction: For access to full text, subscription to the journal or payment for the individual article is required.
    File URL: https://libkey.io/10.2202/1544-6115.1420?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
    ---><---

    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. Ferreira José António & Zwinderman Aeilko H, 2006. "Approximate Power and Sample Size Calculations with the Benjamini-Hochberg Method," The International Journal of Biostatistics, De Gruyter, vol. 2(1), pages 1-38, September.
    2. Ferreira José A. & Zwinderman Aeilko, 2006. "Approximate Sample Size Calculations with Microarray Data: An Illustration," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 5(1), pages 1-18, October.
    3. John P A Ioannidis, 2005. "Why Most Published Research Findings Are False," PLOS Medicine, Public Library of Science, vol. 2(8), pages 1-1, August.
    4. Daniel Yekutieli & Anat Reiner‐Benaim & Yoav Benjamini & Gregory I. Elmer & Neri Kafkafi & Noah E. Letwin & Norman H. Lee, 2006. "Approaches to multiplicity issues in complex research in microarray analysis," Statistica Neerlandica, Netherlands Society for Statistics and Operations Research, vol. 60(4), pages 414-437, November.
    5. John D. Storey & Jonathan E. Taylor & David Siegmund, 2004. "Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: a unified approach," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 66(1), pages 187-205, February.
    6. Joseph Romano & Azeem Shaikh & Michael Wolf, 2008. "Control of the false discovery rate under dependence using the bootstrap and subsampling," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 17(3), pages 417-442, November.
    7. Mette Langaas & Bo Henry Lindqvist & Egil Ferkingstad, 2005. "Estimating the proportion of true null hypotheses, with application to DNA microarray data," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 67(4), pages 555-572, September.
    8. Yoav Benjamini & Yosef Hochberg, 2000. "On the Adaptive Control of the False Discovery Rate in Multiple Testing With Independent Statistics," Journal of Educational and Behavioral Statistics, , vol. 25(1), pages 60-83, March.
    9. Joseph Romano & Azeem Shaikh & Michael Wolf, 2008. "Rejoinder on: Control of the false discovery rate under dependence using the bootstrap and subsampling," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 17(3), pages 461-471, November.
    10. Yekutieli, Daniel, 2008. "Hierarchical False Discovery RateControlling Methodology," Journal of the American Statistical Association, American Statistical Association, vol. 103, pages 309-316, March.
    Full references (including those not matched with items on IDEAS)

    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. Cai, Qingyun, 2018. "A scoring criterion for rejection of clustered p-values," Computational Statistics & Data Analysis, Elsevier, vol. 121(C), pages 180-189.
    2. Bajgrowicz, Pierre & Scaillet, Olivier, 2012. "Technical trading revisited: False discoveries, persistence tests, and transaction costs," Journal of Financial Economics, Elsevier, vol. 106(3), pages 473-491.
    3. Shigeyuki Matsui & Hisashi Noma, 2011. "Estimating Effect Sizes of Differentially Expressed Genes for Power and Sample-Size Assessments in Microarray Experiments," Biometrics, The International Biometric Society, vol. 67(4), pages 1225-1235, December.
    4. Moon, H.R. & Perron, B., 2012. "Beyond panel unit root tests: Using multiple testing to determine the nonstationarity properties of individual series in a panel," Journal of Econometrics, Elsevier, vol. 169(1), pages 29-33.
    5. Matteo M. Galizzi & Daniel Navarro-Martinez, 2019. "On the External Validity of Social Preference Games: A Systematic Lab-Field Study," Management Science, INFORMS, vol. 65(3), pages 976-1002, March.
    6. John A. List & Azeem M. Shaikh & Yang Xu, 2019. "Multiple hypothesis testing in experimental economics," Experimental Economics, Springer;Economic Science Association, vol. 22(4), pages 773-793, December.
    7. Yoav Benjamini, 2010. "Discovering the false discovery rate," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 72(4), pages 405-416, September.
    8. de Uña-Alvarez Jacobo, 2012. "The Beta-Binomial SGoF method for multiple dependent tests," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(3), pages 1-32, May.
    9. Campbell R. Harvey & Yan Liu, 2020. "False (and Missed) Discoveries in Financial Economics," Papers 2006.04269, arXiv.org.
    10. Tim Bancroft & Chuanlong Du & Dan Nettleton, 2013. "Estimation of False Discovery Rate Using Sequential Permutation p-Values," Biometrics, The International Biometric Society, vol. 69(1), pages 1-7, March.
    11. Bryan D. MacGregor & Rainer Schulz & Yuan Zhao, 2021. "Performance and Market Maturity in Mutual Funds: Is Real Estate Different?," The Journal of Real Estate Finance and Economics, Springer, vol. 63(3), pages 437-492, October.
    12. Campbell R. Harvey & Yan Liu, 2020. "False (and Missed) Discoveries in Financial Economics," Journal of Finance, American Finance Association, vol. 75(5), pages 2503-2553, October.
    13. Alexandre Belloni & Victor Chernozhukov & Denis Chetverikov & Christian Hansen & Kengo Kato, 2018. "High-dimensional econometrics and regularized GMM," CeMMAP working papers CWP35/18, Centre for Microdata Methods and Practice, Institute for Fiscal Studies.
    14. Dean Palejev & Mladen Savov, 2021. "On the Convergence of the Benjamini–Hochberg Procedure," Mathematics, MDPI, vol. 9(17), pages 1-19, September.
    15. Becker William & Paruolo Paolo & Saltelli Andrea, 2021. "Variable Selection in Regression Models Using Global Sensitivity Analysis," Journal of Time Series Econometrics, De Gruyter, vol. 13(2), pages 187-233, July.
    16. Qingyun Cai & Hock Peng Chan, 2017. "A Double Application of the Benjamini-Hochberg Procedure for Testing Batched Hypotheses," Methodology and Computing in Applied Probability, Springer, vol. 19(2), pages 429-443, June.
    17. Long Qu & Dan Nettleton & Jack C. M. Dekkers, 2012. "Improved Estimation of the Noncentrality Parameter Distribution from a Large Number of t-Statistics, with Applications to False Discovery Rate Estimation in Microarray Data Analysis," Biometrics, The International Biometric Society, vol. 68(4), pages 1178-1187, December.
    18. Christophe Hurlin & Sébastien Laurent & Rogier Quaedvlieg & Stephan Smeekes, 2017. "Risk Measure Inference," Journal of Business & Economic Statistics, Taylor & Francis Journals, vol. 35(4), pages 499-512, October.
    19. John A. List & Azeem M. Shaikh & Atom Vayalinkal, 2023. "Multiple testing with covariate adjustment in experimental economics," Journal of Applied Econometrics, John Wiley & Sons, Ltd., vol. 38(6), pages 920-939, September.
    20. Chen, Xiongzhi, 2019. "Uniformly consistently estimating the proportion of false null hypotheses via Lebesgue–Stieltjes integral equations," Journal of Multivariate Analysis, Elsevier, vol. 173(C), pages 724-744.

    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:bpj:sagmbi:v:8:y:2009:i:1:n:7. 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: Peter Golla (email available below). General contact details of provider: https://www.degruyter.com .

    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.