NDLI: Assessment of reliability of microarray data and estimation of signal thresholds using mixture modeling

Content Provider	PubMed Central
Author	Asyali, Musa H. Shoukri, Mohamed M. Omer, Demirkaya Khabar, Khalid S. A.
Copyright Year	2004
Abstract	DNA microarray is an important tool for the study of gene activities but the resultant data consisting of thousands of points are error-prone. A serious limitation in microarray analysis is the unreliability of the data generated from low signal intensities. Such data may produce erroneous gene expression ratios and cause unnecessary validation or post-analysis follow-up tasks. In this study, we describe an approach based on normal mixture modeling for determining optimal signal intensity thresholds to identify reliable measurements of the microarray elements and subsequently eliminate false expression ratios. We used univariate and bivariate mixture modeling to segregate the microarray data into two classes, low signal intensity and reliable signal intensity populations, and applied Bayesian decision theory to find the optimal signal thresholds. The bivariate analysis approach was found to be more accurate than the univariate approach; both approaches were superior to a conventional method when validated against a reference set of biological data that consisted of true and false gene expression data. Elimination of unreliable signal intensities in microarray data should contribute to the quality of microarray data including reproducibility and reliability of gene expression ratios.
Related Links	http://dx.doi.org/10.1093/nar/gkh544
Ending Page	2335
Page Count	13
Starting Page	2323
File Format	PDF
ISSN	13624962
e-ISSN	13624962
Journal	Nucleic Acids Research
Issue Number	8
Volume Number	32
Language	English
Publisher	Oxford University Press
Publisher Date	2004-04-28
Access Restriction	Open
Rights Holder	Oxford University Press
Subject Keyword	Genetics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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