IDEAS home Printed from https://ideas.repec.org/a/spr/stabio/v13y2021i2d10.1007_s12561-019-09251-5.html
   My bibliography  Save this article

Robust and Powerful Differential Composition Tests for Clustered Microbiome Data

Author

Listed:
  • Zheng-Zheng Tang

    (University of Wisconsin-Madison, and Wisconsin Institute for Discovery)

  • Guanhua Chen

    (University of Wisconsin-Madison)

Abstract

Thanks to advances in high-throughput sequencing technologies, the importance of microbiome to human health and disease has been increasingly recognized. Analyzing microbiome data from sequencing experiments is challenging due to their unique features such as compositional data, excessive zero observations, overdispersion, and complex relations among microbial taxa. Clustered microbiome data have become prevalent in recent years from designs such as longitudinal studies, family studies, and matched case–control studies. The within-cluster dependence compounds the challenge of the microbiome data analysis. Methods that properly accommodate intra-cluster correlation and features of the microbiome data are needed. We develop robust and powerful differential composition tests for clustered microbiome data. The methods do not rely on any distributional assumptions on the microbial compositions, which provides flexibility to model various correlation structures among taxa and among samples within a cluster. By leveraging the adjusted sandwich covariance estimate, the methods properly accommodate sample dependence within a cluster. The two-part version of the test can further improve power in the presence of excessive zero observations. Different types of confounding variables can be easily adjusted for in the methods. We perform extensive simulation studies under commonly adopted clustered data designs to evaluate the methods. We demonstrate that the methods properly control the type I error under all designs and are more powerful than existing methods in many scenarios. The usefulness of the proposed methods is further demonstrated with two real datasets from longitudinal microbiome studies on pregnant women and inflammatory bowel disease patients. The methods have been incorporated into the R package “miLineage” publicly available at https://tangzheng1.github.io/tanglab/software.html .

Suggested Citation

  • Zheng-Zheng Tang & Guanhua Chen, 2021. "Robust and Powerful Differential Composition Tests for Clustered Microbiome Data," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 13(2), pages 200-216, July.
  • Handle: RePEc:spr:stabio:v:13:y:2021:i:2:d:10.1007_s12561-019-09251-5
    DOI: 10.1007/s12561-019-09251-5
    as

    Download full text from publisher

    File URL: http://link.springer.com/10.1007/s12561-019-09251-5
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.

    File URL: https://libkey.io/10.1007/s12561-019-09251-5?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. Jack A. Gilbert & Robert A. Quinn & Justine Debelius & Zhenjiang Z. Xu & James Morton & Neha Garg & Janet K. Jansson & Pieter C. Dorrestein & Rob Knight, 2016. "Microbiome-wide association studies link dynamic microbial consortia to disease," Nature, Nature, vol. 535(7610), pages 94-103, July.
    2. Robert B. Davies, 1980. "The Distribution of a Linear Combination of χ2 Random Variables," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 29(3), pages 323-333, November.
    3. Patricio S La Rosa & J Paul Brooks & Elena Deych & Edward L Boone & David J Edwards & Qin Wang & Erica Sodergren & George Weinstock & William D Shannon, 2012. "Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-13, December.
    4. Cragg, John G, 1971. "Some Statistical Models for Limited Dependent Variables with Application to the Demand for Durable Goods," Econometrica, Econometric Society, vol. 39(5), pages 829-844, September.
    5. Braun T.M. & Feng Z., 2001. "Optimal Permutation Tests for the Analysis of Group Randomized Trials," Journal of the American Statistical Association, American Statistical Association, vol. 96, pages 1424-1432, December.
    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. Marcén, Miriam & Molina, José Alberto & Morales, Marina, 2018. "The effect of culture on the fertility decisions of immigrant women in the United States," Economic Modelling, Elsevier, vol. 70(C), pages 15-28.
    2. Langyintuo, Augustine S. & Mungoma, Catherine, 2008. "The effect of household wealth on the adoption of improved maize varieties in Zambia," Food Policy, Elsevier, vol. 33(6), pages 550-559, December.
    3. repec:zbw:rwirep:0200 is not listed on IDEAS
    4. Subir K. Chakrabarti & Srikant Devaraj & Pankaj C. Patel, 2021. "Minimum wage and restaurant hygiene violations: Evidence from Seattle," Managerial and Decision Economics, John Wiley & Sons, Ltd., vol. 42(1), pages 85-99, January.
    5. Torres, Marcelo de O. & Felthoven, Ronald G., 2014. "Productivity growth and product choice in catch share fisheries: The case of Alaska pollock," Marine Policy, Elsevier, vol. 50(PA), pages 280-289.
    6. Paul L. Burgess & Stuart A. Low, 1998. "How do Unemployment Insurance and Recall Expectations Affect on-the-job Search among Workers Who Receive Advance Notice of Layoff?," ILR Review, Cornell University, ILR School, vol. 51(2), pages 241-252, January.
    7. Giuseppe Bertola & Luigi Guiso & Luigi Pistaferri, 2005. "Uncertainty and Consumer Durables Adjustment," The Review of Economic Studies, Review of Economic Studies Ltd, vol. 72(4), pages 973-1007.
    8. Silvia Magri, 2014. "Does issuing equity help R&D activity? Evidence from unlisted Italian high-tech manufacturing firms," Economics of Innovation and New Technology, Taylor & Francis Journals, vol. 23(8), pages 825-854, November.
    9. H. T. Tran & E. Santarelli, 2013. "Determinants and Effects of Innovative Activities in Vietnam. A Firm-level Analysis," Working Papers wp909, Dipartimento Scienze Economiche, Universita' di Bologna.
    10. Mather, David & Jayne, Thomas S., 2011. "The Impact of State Marketing Board Operations on Smallholder Behavior and Incomes: The Case of Kenya," Food Security International Development Working Papers 120742, Michigan State University, Department of Agricultural, Food, and Resource Economics.
    11. Glenn W. Harrison & James P. Feehan & Alison C. Edwards & Jorge Segovia, 2003. "Cigarette Smoking and the Cost of Hospital and Physician Care," Canadian Public Policy, University of Toronto Press, vol. 29(1), pages 1-19, March.
    12. Chen, Shu-Ling & Miranda, Mario J., 2006. "Modeling Yield Distribution In High Risk Counties: Application To Texas Upland Cotton," 2006 Annual meeting, July 23-26, Long Beach, CA 21392, American Agricultural Economics Association (New Name 2008: Agricultural and Applied Economics Association).
    13. Gunter, Samara, 2013. "State Earned Income Tax Credits and Participation in Regular and Informal Work," National Tax Journal, National Tax Association;National Tax Journal, vol. 66(1), pages 33-62, March.
    14. Xiaozhen Lai & Hongguo Rong & Xiaochen Ma & Zhiyuan Hou & Shunping Li & Rize Jing & Haijun Zhang & Yun Lyu & Jiahao Wang & Huangyufei Feng & Zhibin Peng & Luzhao Feng & Hai Fang, 2021. "The Economic Burden of Influenza-Like Illness among Children, Chronic Disease Patients, and the Elderly in China: A National Cross-Sectional Survey," IJERPH, MDPI, vol. 18(12), pages 1-16, June.
    15. Bhattacharjee, Manojit & Rajeev, Meenakshi, 2014. "Is access to loan adequate for financing capital expenditure?: A household level analysis on some selected states of India," Working Papers 315, Institute for Social and Economic Change, Bangalore.
    16. Henk-Wim de Boer, 2015. "A structural analysis of labour supply and involuntary unemployment in the Netherlands," CPB Discussion Paper 312.rdf, CPB Netherlands Bureau for Economic Policy Analysis.
    17. Hüttel, Silke & Mußhoff, Oliver & Odening, Martin & Zinych, Nataliya, 2008. "Estimating investment equations in imperfect capital markets," SFB 649 Discussion Papers 2008-016, Humboldt University Berlin, Collaborative Research Center 649: Economic Risk.
    18. Khadjavi, Menusch & Lange, Andreas & Nicklisch, Andreas, 2014. "The Social Value of Transparency and Accountability: Experimental Evidence from Asymmetric Public Good Games," VfS Annual Conference 2014 (Hamburg): Evidence-based Economic Policy 100512, Verein für Socialpolitik / German Economic Association.
    19. Richard Mussa, 2013. "Rural--urban differences in parental spending on children's primary education in Malawi," Development Southern Africa, Taylor & Francis Journals, vol. 30(6), pages 789-811, December.
    20. Wongnaa, Camillus Abawiera & Kyei, Afrane Baffour & Apike, Isaac Akurugu & Awunyo-Vitor, Dadson & Dziwornu, Raymond K., 2021. "Perception and Adoption of Artificial Pollination Technology in Cocoa Production: Evidence from Ghana," 2021 Conference, August 17-31, 2021, Virtual 314939, International Association of Agricultural Economists.
    21. Steven Yen, 1995. "Alternative transformations in a class of limited dependent variable models: alcohol consumption by US women," Applied Economics Letters, Taylor & Francis Journals, vol. 2(8), pages 258-262.

    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:spr:stabio:v:13:y:2021:i:2:d:10.1007_s12561-019-09251-5. 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: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.springer.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.