TY - JOUR
T1 - MethylAid
T2 - Visual and interactive quality control of large Illumina 450k datasets
AU - Van Iterson, Maarten
AU - Tobi, Elmar W.
AU - Slieker, Roderick C.
AU - Den Hollander, Wouter
AU - Luijk, René
AU - Slagboom, P. Eline
AU - Heijmans, Bastiaan T.
PY - 2014/1/1
Y1 - 2014/1/1
N2 - Summary: 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.
AB - Summary: 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.
UR - http://www.scopus.com/inward/record.url?scp=84925550941&partnerID=8YFLogxK
U2 - https://doi.org/10.1093/bioinformatics/btu566
DO - https://doi.org/10.1093/bioinformatics/btu566
M3 - Article
C2 - 25147358
SN - 1367-4803
VL - 30
SP - 3435
EP - 3437
JO - Bioinformatics
JF - Bioinformatics
IS - 23
ER -