illuminaio: An open source IDAT parsing tool for Illumina microarrays.
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 data in public databases, in the same way that the CEL file serves as the standard for the Affymetrix platform.
CRUK Cambridge Institute, Li Ka Shing Centre, The University of Cambridge, Cambridge, CB2 0RE, UK.
Mike L
ML
Smith
Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Keith A
KA
Baggerly
Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94107, USA.
Henrik
H
Bengtsson
Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia ; Department of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria 3052, Australia.
Matthew E
ME
Ritchie
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA ; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
Kasper D
KD
Hansen