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Improved processing of microarray data using image reconstruction techniques

O'Neill, P. and Magoulas, George D. and Liu, X. (2003) Improved processing of microarray data using image reconstruction techniques. IEEE Transactions on Nanobioscience 2 (4), pp. 176-183. ISSN 1536-1241.

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Official URL: http://dx.doi.org/10.1109/TNB.2003.817022

Abstract

Spotted cDNA microarray data analysis suffers from various problems such as noise from a variety of sources, missing data, inconsistency, and, of course, the presence of outliers. This paper introduces a new method that dramatically reduces the noise when processing the original image data. The proposed approach recreates the microarray slide image, as it would have been with all the genes removed. By subtracting this background recreation from the original, the gene ratios can be calculated with more precision and less influence from outliers and other artifacts that would normally make the analysis of this data more difficult. The new technique is also beneficial, as it does not rely on the accurate fitting of a region to each gene, with its only requirement being an approximate coordinate. In experiments conducted, the new method was tested against one of the mainstream methods of processing spotted microarray images. Our method is shown to produce much less variation in gene measurements. This evidence is supported by clustering results that show a marked improvement in accuracy.

Item Type: Article
Additional Information: This is an exact copy of a paper published in IEEE Transactions on Nanobioscience (ISSN 1536-1241). It is reproduced with permission from the publisher. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. © 2003 IEEE. Copyright and all rights therein are retained by authors or by other copyright holders. All persons downloading this information are expected to adhere to the terms and constraints invoked by copyright. This document or any part thereof may not be reposted without the explicit permission of the copyright holder.
Keyword(s) / Subject(s): Data quality, image, microarray, preprocessing,reconstruction
School or Research Centre: Birkbeck Schools and Research Centres > School of Business, Economics & Informatics > Computer Science and Information Systems
Depositing User: Sandra Plummer
Date Deposited: 17 Jan 2006
Last Modified: 17 Apr 2013 12:32
URI: http://eprints.bbk.ac.uk/id/eprint/298

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