Introduction

DNA methylation patterns are well known to vary substantially across cell types or tissues. Hence, existing normalization methods may not be optimal if they do not take this into account. We therefore present a new R package for normalization of data from the Illumina Infinium Human Methylation450 BeadChip (Illumina 450 K) built on the concepts in the recently published funNorm method, and introducing cell-type or tissue-type flexibility.funtooNorm is relevant for data sets containing samples from two or more cell or tissue types. A visual display of cross-validated errors informs the choice of the optimal number of components in the normalization. Benefits of cell (tissue)-specific normalization are demonstrated in three data sets. Improvement can be substantial; it is strikingly better on chromosome X, where methylation patterns have unique inter-tissue variability.An R package is available at https://github.com/GreenwoodLab/funtooNorm, and has been submitted to Bioconductor at http://bioconductor.org.

Publications

  1. funtooNorm: an R package for normalization of DNA methylation data when there are multiple cell or tissue types.
    Cite this
    Oros Klein K, Grinek S, Bernatsky S, Bouchard L, Ciampi A, Colmegna I, Fortin JP, Gao L, Hivert MF, Hudson M, Kobor MS, Labbe A, MacIsaac JL, Meaney MJ, Morin AM, O'Donnell KJ, Pastinen T, Van Ijzendoorn MH, Voisin G, Greenwood CM, 2016-02-01 - Bioinformatics (Oxford, England)

Credits

  1. Kathleen Oros Klein
    Developer

    Lady Davis Institute, Jewish General Hospital, Canada

  2. Stepan Grinek
    Developer

    Lady Davis Institute, Jewish General Hospital, Canada

  3. Sasha Bernatsky
    Developer

    Divisions of Rheumatology and Clinical Epidemiology, McGill University Health Centre, Canada

  4. Luigi Bouchard
    Developer

    ECOGENE-21, Centre intégré universitaire de santé et de service sociaux du Saguenay-Lac-Saint-Jean, Canada

  5. Antonio Ciampi
    Developer

    Department of Epidemiology, Biostatistics and Occupational Health, Canada

  6. Ines Colmegna
    Developer

    Division of Experimental Medicine, McGill University Health Centre, Canada

  7. Jean-Philippe Fortin
    Developer

    Department of Biostatistics, Johns Hopkins University, United States of America

  8. Long Gao
    Developer

    Department of Epidemiology, Biostatistics and Occupational Health, Canada

  9. Marie-France Hivert
    Developer

    Department of Population Medicine, Harvard Medical School, Canada

  10. Marie Hudson
    Developer

    Lady Davis Institute, Jewish General Hospital, Canada

  11. Michael S Kobor
    Developer

    Canadian Institute for Advanced Research, Child, Canada

  12. Aurelie Labbe
    Developer

    Department of Epidemiology, Biostatistics and Occupational Health, Canada

  13. Julia L MacIsaac
    Developer

    Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Canada

  14. Michael J Meaney
    Developer

    Ludmer Center for Neuroinformatics and Mental Health, Canadian Institute for Advanced Research, Canada

  15. Alexander M Morin
    Developer

    Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Canada

  16. Kieran J O'Donnell
    Developer

    Douglas Mental Health University Institute, McGill University, Canada

  17. Tomi Pastinen
    Developer

    Department of Human Genetics, McGill University, Canada

  18. Marinus H Van Ijzendoorn
    Developer

    Centre for Child and Family Studies, Leiden University

  19. Gregory Voisin
    Developer

    Lady Davis Institute, Jewish General Hospital, Canada

  20. Celia M T Greenwood
    Investigator

    Lady Davis Institute, Jewish General Hospital, Canada

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Summary
AccessionBT002252
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionCanada
Submitted ByCelia M T Greenwood