Unlock your biological data
As for their many other BeadArray platforms, Illumina methylation data is usually obtained in the form of Intensity Data (IDAT) Files. This is a proprietary format that is output by the scanner and stores summary intensities for each probe on the array. However, there are Bioconductor packages available that facilitate the import of data from IDAT files into R (Smith et al., 2013).
(Smith et al., 2013) illuminaio: An open source IDAT parsing tool for Illumina microarrays. F1000Res.