The IDAT file format is used to store BeadArray data from the myriad of genomewide profiling platforms on offer from Illumina Inc. This proprietary format is output directly from the scanner and stores summary intensities for each probe-type on an array in a compact manner. A lack of open source tools to process IDAT files has hampered their uptake by the research community beyond the standard step of using the vendor’s software to extract the data they contain in a human readable text format. To fill this void, we have developed the illuminaio package that parses IDAT files from any BeadArray platform, including the decryption of files from Illumina’s gene expression arrays. illuminaio provides the first open-source package for this task, and will promote wider uptake of the IDAT format as a standard for sharing Illumina BeadArray presents an R package to process IDAT files, the file format of et al. Illumina BeadArrays. The package fills an important gap in data processing by enabling the illuminaio analysis of Illumina data without Illumina software. The gap is illustrated when the authors cite the disparity between the availability of CEL files (Affymetrix file format) and IDAT files in public data repositories. In addition to eliminating the need to use Illumina software, extracts additional illuminaio information from the IDAT files allowing improved quality control analyses and additional data correction algorithms. the simplified analysis describes illuminaio, an R package to process the raw data files produced by the Illumina scanning software. This tool is valuable, because it enables researchers to use a completely open analysis workflow, without having to use a closed source, blackbox, analysis step. tried the package on IDAT files from several chiptypes, and only files from the beginning of 2005 scanned with beadscan 2.2 were rejected. Files scanned with beadscan 2.3 (Nov 2005) and onwards were processed properly.
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