MethylAid

MethylAid performs quality control on Illumina 450k array DNA methylation data to identify poor-quality samples and annotate technical variation for large-scale genome-wide DNA methylation studies.

Key Features:

• Quality control probes: Employs both sample-dependent and sample-independent quality control probes present on the Illumina 450k array to detect poor-quality samples.
• User-adjustable thresholds: Supports user-defined thresholds to tailor detection criteria for suboptimal samples.
• Diagnostic plots: Produces diagnostic plots to visualize sample-level quality metrics for detection of problematic samples.
• Metadata annotation: Enables annotation of plots with metadata such as batch information to aid identification of batch effects and outliers.
• Scalability: Designed to handle large-scale studies, making it suitable for extensive epigenome-wide association studies (EWAS).
• Implementation: Implemented as an R/Bioconductor package.

Scientific Applications:

• Quality assessment: Used for sample-level quality assessment in DNA methylation studies prior to downstream analysis.
• Large-scale and multi-batch studies: Applied in large-scale EWAS and multi-batch experimental designs to detect technical artifacts, batch effects, and outliers.

Methodology:

MethylAid is implemented as an R/Bioconductor package and leverages sample-dependent and sample-independent Illumina 450k quality control probes together with user-defined thresholds to identify poor-quality samples, producing diagnostic plots and supporting metadata annotation.