IDEAS home Printed from https://ideas.repec.org/a/jss/jstsof/v065i09.html
   My bibliography  Save this article

Mann-Whitney Type Tests for Microarray Experiments: The R Package gMWT

Author

Listed:
  • Fischer, Daniel
  • Oja, Hannu

Abstract

We present the R package gMWT which is designed for the comparison of several treatments (or groups) for a large number of variables. The comparisons are made using certain probabilistic indices (PI). The PIs computed here tell how often pairs or triples of observations coming from different groups appear in a specific order of magnitude. Classical two and several sample rank test statistics such as the Mann-Whitney-Wilcoxon, Kruskal-Wallis, or Jonckheere-Terpstra test statistics are simple functions of these PI. Also new test statistics for directional alternatives are provided. The package gMWT can be used to calculate the variable-wise PI estimates, to illustrate their multivariate distribution and mutual dependence with joint scatterplot matrices, and to construct several classical and new rank tests based on the PIs. The aim of the paper is first to briefly explain the theory that is necessary to understand the behavior of the estimated PIs and the rank tests based on them. Second, the use of the package is described and illustrated with simulated and real data examples. It is stressed that the package provides a new flexible toolbox to analyze large gene or microRNA expression data sets, collected on microarrays or by other high-throughput technologies. The testing procedures can be used in an eQTL analysis, for example, as implemented in the package GeneticTools.

Suggested Citation

  • Fischer, Daniel & Oja, Hannu, 2015. "Mann-Whitney Type Tests for Microarray Experiments: The R Package gMWT," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 65(i09).
    • Handle: RePEc:jss:jstsof:v:065:i09
    DOI: http://hdl.handle.net/10.18637/jss.v065.i09
    as

    Download full text from publisher

    File URL: https://www.jstatsoft.org/index.php/jss/article/view/v065i09/v65i09.pdf
    Download Restriction: no
    File URL: https://www.jstatsoft.org/index.php/jss/article/downloadSuppFile/v065i09/gMWT_1.0.tar.gz
    Download Restriction: no
    File URL: https://www.jstatsoft.org/index.php/jss/article/downloadSuppFile/v065i09/v65i09.R
    Download Restriction: no
    File URL: https://www.jstatsoft.org/index.php/jss/article/downloadSuppFile/v065i09/v65i09-data.zip
    Download Restriction: no
    File URL: https://libkey.io/http://hdl.handle.net/10.18637/jss.v065.i09?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. Eddelbuettel, Dirk & Sanderson, Conrad, 2014. "RcppArmadillo: Accelerating R with high-performance C++ linear algebra," Computational Statistics & Data Analysis, Elsevier, vol. 71(C), pages 1054-1063.
    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. Edgar Brunner & Frank Konietschke & Markus Pauly & Madan L. Puri, 2017. "Rank-based procedures in factorial designs: hypotheses about non-parametric treatment effects," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 79(5), pages 1463-1485, November.

    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. Wilson J. Wright & Peter N. Neitlich & Alyssa E. Shiel & Mevin B. Hooten, 2022. "Mechanistic spatial models for heavy metal pollution," Environmetrics, John Wiley & Sons, Ltd., vol. 33(8), December.
    2. Bachoc, François & Genton, Mark G. & Nordhausen, Klaus & Ruiz-Gazen, Anne & Virta, Joni, 2019. "Spatial Blind Source Separation," TSE Working Papers 19-998, Toulouse School of Economics (TSE).
    3. Napoleón Vargas Jurado & Kent M. Eskridge & Stephen D. Kachman & Ronald M. Lewis, 2018. "Using a Bayesian Hierarchical Linear Mixing Model to Estimate Botanical Mixtures," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 23(2), pages 190-207, June.
    4. James Joseph Balamuta & Steven Andrew Culpepper, 2022. "Exploratory Restricted Latent Class Models with Monotonicity Requirements under PÒLYA–GAMMA Data Augmentation," Psychometrika, Springer;The Psychometric Society, vol. 87(3), pages 903-945, September.
    5. Athanasios C. Micheas & Jiaxun Chen, 2018. "sppmix: Poisson point process modeling using normal mixture models," Computational Statistics, Springer, vol. 33(4), pages 1767-1798, December.
    6. Andrii ROSKLADKA & Roman BAIEV, 2021. "Digitalization of data analysis tools as the key for success in the online trading markets," Access Journal, Access Press Publishing House, vol. 2(3), pages 222-233, September.
    7. Etienne Côme & Nicolas Jouvin & Pierre Latouche & Charles Bouveyron, 2021. "Hierarchical clustering with discrete latent variable models and the integrated classification likelihood," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 15(4), pages 957-986, December.
    8. Mihai C. Giurcanu, 2017. "Oracle M-Estimation for Time Series Models," Journal of Time Series Analysis, Wiley Blackwell, vol. 38(3), pages 479-504, May.
    9. Aaron T L Lun & Hervé Pagès & Mike L Smith, 2018. "beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types," PLOS Computational Biology, Public Library of Science, vol. 14(5), pages 1-15, May.
    10. Tilman M. Davies & Sudipto Banerjee & Adam P. Martin & Rose E. Turnbull, 2022. "A nearest‐neighbour Gaussian process spatial factor model for censored, multi‐depth geochemical data," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 71(4), pages 1014-1043, August.
    11. Jean-Jacques Forneron, 2019. "A Sieve-SMM Estimator for Dynamic Models," Papers 1902.01456, arXiv.org, revised Jan 2023.
    12. Enrique Martínez García & Efthymios Pavlidis & Kostas Vasilopoulos, 2020. "exuber: Recursive Right-Tailed Unit Root Testing with R," Globalization Institute Working Papers 383, Federal Reserve Bank of Dallas, revised 19 Oct 2021.
    13. Savitsky, Terrance & Paddock, Susan, 2014. "Bayesian Semi- and Non-Parametric Models for Longitudinal Data with Multiple Membership Effects in R," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 57(i03).
    14. Battauz, Michela & Vidoni, Paolo, 2022. "A likelihood-based boosting algorithm for factor analysis models with binary data," Computational Statistics & Data Analysis, Elsevier, vol. 168(C).
    15. Cardona Jiménez, Johnatan & de B. Pereira, Carlos A., 2021. "Assessing dynamic effects on a Bayesian matrix-variate dynamic linear model: An application to task-based fMRI data analysis," Computational Statistics & Data Analysis, Elsevier, vol. 163(C).
    16. Andrew Chesher & Adam Rosen & Zahra Siddique, 2019. "Estimating Endogenous Effects on Ordinal Outcomes," CeMMAP working papers CWP66/19, Centre for Microdata Methods and Practice, Institute for Fiscal Studies.
    17. He, Xuming & Pan, Xiaoou & Tan, Kean Ming & Zhou, Wen-Xin, 2023. "Smoothed quantile regression with large-scale inference," Journal of Econometrics, Elsevier, vol. 232(2), pages 367-388.
    18. Loy, Adam & Hofmann, Heike, 2014. "HLMdiag: A Suite of Diagnostics for Hierarchical Linear Models in R," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 56(i05).
    19. Kenneth A. Flagg & Andrew Hoegh & John J. Borkowski, 2020. "Modeling Partially Surveyed Point Process Data: Inferring Spatial Point Intensity of Geomagnetic Anomalies," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 25(2), pages 186-205, June.
    20. Lu Chen & Balgobin Nandram, 2023. "Bayesian Logistic Regression Model for Sub-Areas," Stats, MDPI, vol. 6(1), pages 1-23, January.

    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:jss:jstsof:v:065:i09. 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: Christopher F. Baum (email available below). General contact details of provider: http://www.jstatsoft.org/ .

    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.