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Bioinformatics Advance Access published online on August 25, 2006
Bioinformatics, 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
Received July 10, 2006
Revised August 18, 2006
Accepted August 22, 2006

Applications note

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.
Kellie J. Archer, E-mail: kjarcher{at}vcu.edu


  Abstract

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 previously demonstrated by 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.

Associate Editor: Trey Ideker
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