illuminaio: An open source IDAT parsing tool for Illumina microarrays[v1; ref status: indexed, http://f1000r.es/2f5]
- Author(s)
- Smith, ML; Baggerly, KA; Bengtsson, H; Ritchie, ME;
- Journal Title
- F1000 Research
- Publication Type
- Journal Article
- Abstract
- 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
- Publisher
- F1000
- Research Division(s)
- Molecular Medicine
- Publisher's Version
- https://doi.org/10.12688/f1000research.2-264.v
- Open Access at Publisher's Site
http://f1000research.com/articles/2-264/v1- Terms of Use/Rights Notice
- Copyright: © 2013 Smith ML et al. This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Data associated with the article are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication).
Creation Date: 2014-02-26 11:46:55