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Bioinformatics Advance Access originally published online on August 25, 2006
Bioinformatics 2006 22(21):2699-2701; doi:10.1093/bioinformatics/btl459
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

An application for assessing quality of RNA hybridized to Affymetrix GeneChips

Kellie J. Archer 1,* and Tobias Guennel 2

1 Department of Biostatistics, Virginia Commonwealth University Richmond, VA 23298-0032, USA
2 Technische Universität Chemnitz, 09107 Chemnitz Germany

*To whom correspondence should be addressed.

Summary: This paper describes a stand-alone application for estimating the 3' to 5' ratio by fitting a mixed effects model to the interior pixel intensities of perfect match probes for selected control probe sets from an Affymetrix *.DAT file. The effectiveness of this method was demonstrated previously by an application of the method to two microarray datasets for which external verification of RNA quality was known. This application provides a more objective assessment of sample quality in that both a point estimate and 95% confidence interval about the 3' to 5' ratio are provided.

Availability: The software and installation instructions are freely available for download at http://www.people.vcu.edu/~kjarcher/Research/Data.htm

Contact: kjarcher{at}vcu.edu

Received on July 10, 2006; revised on August 18, 2006; accepted on August 22, 2006

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