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Bioinformatics Advance Access published online on April 26, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm127
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

libaffy: Software for Processing Affymetrix GeneChip Data

Steven A. Eschrich 1,* and Andrew M. Hoerter 1

1H. Lee Moffitt Cancer Center and Research Institute, University of South Florida, Tampa, FL 33612, USA.

*To whom correspondence should be addressed. Steven A. Eschrich, E-mail: EschriS{at}moffitt.usf.edu


  Abstract

Summary: Affymetrix GeneChip microarrays are increasingly used in gene expression studies and in greater number. A software library was developed that supports Affymetrix file formats and implements two popular summary algorithms (MAS5.0 and RMA). The library is modular in design for integration into larger systems and processing pipelines. Additionally, a graphical interface (GENE) was developed to allow end-user access to the functionality within the library.

Availability: libaffy is free to use under the GNU GPL license. The source code and Windows binaries can be freely accessed from the website http://src.moffitt.usf.edu/libaffy. Additional API documentation and user manual are available.

Associate Editor: Dr. Olga Troyanskaya

Received on December 13, 2006; revised on February 23, 2007; accepted on March 25, 2007

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