affyPara - a Bioconductor Package for Parallelized Preprocessing Algorithms of Affymetrix Microarray Data

• Published in: Bioinformatics and biology insights Vol. 2009; no. 3; pp. BBI.S3060 - 87
• Main Authors: Schmidberger, Markus, Vicedo, Esmeralda, Mansmann, Ulrich
• Format: Journal Article
• Language: English
• Published: London, England SAGE Publishing 01.01.2009; SAGE Publications; Sage Publications Ltd. (UK); Sage Publications Ltd; Libertas Academica
• Subjects: Algorithms; Arrays; Computation; Licenses; Packages; Parallel processing; Partitions; Preprocessing; Short Report; R; microarray; preprocessing; normalization; parallel computing
• ISSN: 1177-9322; 1177-9322
• DOI: 10.4137/BBI.S3060

Markus Schmidberger, Esmeralda Vicedo and Ulrich MansmannDivision of Biometrics and Bioinformatics, IBE, University of Munich, 81377 Munich, Germany. AbstractMicroarray data repositories as well as large clinical applications of gene expression allow to analyse several hundreds of microarrays at one time. The preprocessing of large amounts of microarrays is still a challenge. The algorithms are limited by the available computer hardware. For example, building classification or prognostic rules from large microarray sets will be very time consuming. Here, preprocessing has to be a part of the cross-validation and resampling strategy which is necessary to estimate the rule's prediction quality honestly. This paper proposes the new Bioconductor package affyPara for parallelized preprocessing of Affymetrix microarray data. Partition of data can be applied on arrays and parallelization of algorithms is a straightforward consequence. The partition of data and distribution to several nodes solves the main memory problems and accelerates preprocessing by up to the factor 20 for 200 or more arrays. affyPara is a free and open source package, under GPL license, available form the Bioconductor project at www.bioconductor.org. A user guide and examples are provided with the package.