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Biostatistics Advance Access published online on August 31, 2005
Biostatistics, doi:10.1093/biostatistics/kxj001
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© The Author 2005. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oupjournals.org.
Received May 3, 2005
Revised August 22, 2005
Accepted August 30, 2005

Article

Assessing quality of hybridized RNA in Affymetrix GeneChip experiments using mixed effects models

Kellie J. Archer 1*, Catherine I. Dumur 2, Suresh E. Joel 3, and Viswanathan Ramakrishnan 1

1 Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298-0032, U.S.A
2 Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298-0248, U.S.A
3 Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, VA 23298-0694, U.S.A

* To whom correspondence should be addressed.
Kellie J. Archer, E-mail: kjarcher{at}vcu.edu


  Abstract

The technology for hybridizing archived tissue specimens and the use of laser capture microdissection for selecting cell populations for RNA extraction has increased over the past few years. Both of these methods contribute to RNA degradation. Therefore, quality assessments of RNA hybridized to microarrays is becoming increasingly more important. Existing methods for estimating the quality of RNA hybridized to a GeneChip, from resulting microarray data, suffer from subjectivity and lack of estimates of variability. In this article, a method for assessing RNA quality for a hybridized array which overcomes these drawbacks is proposed. The effectiveness of the proposed method is demonstrated by application of the method to two microarray datasets for which external verification of RNA quality is known.

Keywords: microarray; mixed effects model; degradation; quality; pixel intensities.
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