title: MethylAid: visual and interactive quality control of large Illumina 450k datasets.
abstract: 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.
  
  
  METHODS
  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.
authors.affiliation: Department of Molecular Epidemiology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands.
authors.forename: Maarten
authors.initials: M
authors.lastname: van Iterson
authors.affiliation: Department of Molecular Epidemiology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands.
authors.forename: Elmar W
authors.initials: EW
authors.lastname: Tobi
authors.affiliation: Department of Molecular Epidemiology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands.
authors.forename: Roderick C
authors.initials: RC
authors.lastname: Slieker
authors.affiliation: Department of Molecular Epidemiology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands.
authors.forename: Wouter
authors.initials: W
authors.lastname: den Hollander
authors.affiliation: Department of Molecular Epidemiology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands.
authors.forename: René
authors.initials: R
authors.lastname: Luijk
authors.affiliation: Department of Molecular Epidemiology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands.
authors.forename: P Eline
authors.initials: PE
authors.lastname: Slagboom
authors.affiliation: Department of Molecular Epidemiology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands.
authors.forename: Bastiaan T
authors.initials: BT
authors.lastname: Heijmans
mesh_terms: D019175:DNA Methylation; D023281:Genomics / Q000379:methods; D006801:Humans; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D011786:Quality Control; D012984:Software