Introduction

The Illumina 450k array is a frequently used platform for large-scale genome-wide DNA methylation studies, i.e. epigenome-wide association studies. Currently, quality control of 450k data can be performed with Illumina's GenomeStudio and is part of a limited number 450k analysis pipelines. However, GenomeStudio cannot handle large-scale studies, and existing pipelines provide limited options for quality control and neither support interactive exploration by the user. To aid the detection of bad-quality samples in large-scale genome-wide DNA methylation studies as flexible and transparent as possible, we have developed MethylAid; a visual and interactive Web application using RStudio's shiny package. Bad-quality samples are detected using sample-dependent and sample-independent quality control probes present on the array and user-adjustable thresholds. In-depth exploration of bad-quality samples can be performed using several interactive diagnostic plots. Furthermore, plots can be annotated with user-provided metadata, for example, to identify outlying batches. Our new tool makes quality assessment of 450k array data interactive, flexible and efficient and is, therefore, expected to be useful for both data analysts and core facilities.MethylAid is implemented as an R/Bioconductor package (www.bioconductor.org/packages/3.0/bioc/html/MethylAid.html). A demo application is available from shiny.bioexp.nl/MethylAid.

Publications

  1. MethylAid: visual and interactive quality control of large Illumina 450k datasets.
    Cite this
    van Iterson M, Tobi EW, Slieker RC, den Hollander W, Luijk R, Slagboom PE, Heijmans BT, 2014-12-01 - Bioinformatics (Oxford, England)

Credits

  1. Maarten van Iterson
    Developer

    Department of Molecular Epidemiology, Leiden University Medical Center, United States of America

  2. Elmar W Tobi
    Developer

    Department of Molecular Epidemiology, Leiden University Medical Center, United States of America

  3. Roderick C Slieker
    Developer

    Department of Molecular Epidemiology, Leiden University Medical Center, United States of America

  4. Wouter den Hollander
    Developer

    Department of Molecular Epidemiology, Leiden University Medical Center, United States of America

  5. René Luijk
    Developer

    Department of Molecular Epidemiology, Leiden University Medical Center, United States of America

  6. P Eline Slagboom
    Developer

    Department of Molecular Epidemiology, Leiden University Medical Center, United States of America

  7. Bastiaan T Heijmans
    Investigator

    Department of Molecular Epidemiology, Leiden University Medical Center, United States of America

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Summary
AccessionBT001114
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByBastiaan T Heijmans