Improved processing of microarray data using image reconstruction techniques

IEEE Transactions on Nanobioscience
Paul O'NeillXiaohui Liu

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.

References

Aug 1, 1997·Journal of the American Podiatric Medical Association·M I Altman
Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
Dec 5, 2000·Molecular Biology of the Cell·A P GaschP O Brown
May 8, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·M A NewtonK W Tsui
Jun 5, 2001·Nature Reviews. Genetics·J Quackenbush
Mar 26, 2002·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Charles KooperbergToshio Tsukiyama
Oct 1, 1997·Journal of Biomedical Optics·Y ChenM L Bittner

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Citations

Jul 10, 2008·Bio Systems·Dan V NicolauPhilip K Maini
Apr 25, 2014·IEEE Journal of Biomedical and Health Informatics·Lakshmi SrinivasanSoontorn Oraintara
Jun 17, 2008·IEEE Transactions on Nanobioscience·P SarderS L Stanley
Jun 11, 2011·IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society·Bachar ZineddinXiaohui Liu
Apr 8, 2010·IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society·Tamanna Howlader, Yogendra P Chaubey
Jan 6, 2005·IEEE Transactions on Nanobioscience·Rastislav LukacAnastasios N Venetsanopoulos
Jul 11, 2006·Comparative Biochemistry and Physiology. Toxicology & Pharmacology : CBP·Zhenlin JuRonald B Walter
Apr 23, 2005·Bioinformatics·Qunhua LiAdrian E Raftery

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