minfi

minfi performs analysis and visualization of Illumina Infinium DNA methylation array data for HumanMethylation450 ('450k') and HumanMethylationEPIC ('EPIC') arrays to support integration and normalization across these platforms.

Key Features:

• Platform Support: Supports analysis of Illumina Infinium HumanMethylation450 ('450k') and HumanMethylationEPIC ('EPIC') array data within a unified framework.
• Visualization: Provides visualization capabilities for DNA methylation data derived from Infinium arrays.
• Normalization Methods: Implements the single-sample Noob (ssNoob) normalization method for processing individual arrays.
• Preprocessing: Enables incremental preprocessing of individual methylation arrays using ssNoob to maintain consistency across samples.
• Joint Analysis and Normalization: Facilitates joint analysis and normalization of 450k and EPIC platform data for comparative studies.

Scientific Applications:

• Data Integration: Integrates datasets from different generations of Illumina methylation arrays to support longitudinal and large-scale epigenetic studies.
• Comparative Studies and Meta-analysis: Enables comparative analyses and meta-analyses across 450k and EPIC datasets through joint normalization.
• Cell Type Composition Estimation: Estimates cell type composition in samples using reference 450k datasets to account for cellular heterogeneity in methylation analyses.

Methodology:

Uses preprocessing, normalization, and analysis of Illumina Infinium methylation data including the single-sample Noob (ssNoob) method and procedures for joint normalization of 450k and EPIC arrays.