Bioinformatics Vol. 18 no. 5 2002
Pages 747-756
© 2002 Oxford University Press
Unsupervised technique for robust target separation and analysis of DNA microarray spots through adaptive pixel clustering
1 Center for Human Molecular Genetics,
University of Nebraska Medical Center, Omaha, NE 68198, USA
2 Department of Statistics, University of
California, Berkeley, CA 94720, USA
Received on August 9, 2001
; revised on November 8, 2001 and December 4, 2001
; accepted on December 12, 2001
Motivation: Microarray images challenge existing analytical methods in many ways given that gene spots are often comprised of characteristic imperfections. Irregular contours, donut shapes, artifacts, and low or heterogeneous expression impair corresponding values for red and green intensities as well as their ratio R/G. New approaches are needed to ensure accurate data extraction from these images.
Results: Herein we introduce a novel method for intensity assessment of gene spots. The technique is based on clustering pixels of a target area into foreground and background. For this purpose we implemented two clustering algorithms derived from k-means and Partitioning Around Medoids (PAM), respectively. Results from the analysis of real gene spots indicate that our approach performs superior to other existing analytical methods. This is particularly true for spots generally considered as problematic due to imperfections or almost absent expression. Both PXPAM and PXKMEANS prove to be highly robust against various types of artifacts through adaptive partitioning, which more correctly assesses expression intensity values.
Availability: The implementation of this method is a combination of two complementary tools Extractiff (Java) and Pixclust (free statistical language R), which are available upon request from the authors.
Contact: dbozinov{at}unmc.edu
* To whom correspondence should be addressed.
Both authors contributed equally to
this manuscript.
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