minfi

The minfi package, a widely used tool for analyzing Illumina DNA methylation array data, has been modified to support Illumina's HumanMethylationEPIC ('EPIC') array. This update includes methods for the joint analysis and normalization of data from the HumanMethylation450 ('450k') and EPIC platforms. A new single-sample normalization procedure called Noob (ssNoob) is introduced, designed explicitly for incremental preprocessing of individual methylation arrays, recommended when integrating data from multiple generations of Infinium methylation arrays. The modified minfi package also allows for estimating cell type composition for EPIC arrays using reference 450k datasets. These updates ensure that minfi provides the necessary tools for effectively integrating existing and forthcoming Illumina methylation array data.