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Biostatistics Advance Access originally published online on August 31, 2005
Biostatistics 2006 7(2):198-212; 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.

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

Kellie J. Archer*

Department of Biostatistics, Virginia Commonwealth University, Sanger Hall B1-066, 1101 East Marshall Street, Richmond, VA 23298-0032, USA kjarcher{at}vcu.edu

Catherine I. Dumur

Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298-0248, USA

Suresh E. Joel

Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, VA 23298-0694, USA

Viswanathan Ramakrishnan

Department of Biostatistics, Virginia Commonwealth University, Sanger Hall B1-066, 1101 East Marshall Street, Richmond, VA 23298-0032, USA

* To whom correspondence should be addressed.

The technology for hybridizing archived tissue specimens and the use of laser-capture microdissection for selecting cell populations for RNA extraction have increased over the past few years. Both these methods contribute to RNA degradation. Therefore, quality assessments of RNA hybridized to microarrays are 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 the application of the method to two microarray data sets for which external verification of RNA quality is known.

Keywords: Degradation; Microarray; Mixed-effects model; Pixel intensities; Quality


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