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A survey of spatial defects in Homo Sapiens Affymetrix GeneChips

Langdon, WB and Upton, GJG and Da Silva Camargo, R and Harrison, AP (2010) 'A survey of spatial defects in Homo Sapiens Affymetrix GeneChips.' IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7 (4). 647 - 653. ISSN 1545-5963

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Abstract

Modern biology has moved from a science of individual measurements to a science where data are collected on an industrial scale. Foremost, among the new tools for biochemistry are chip arrays which, in one operation, measure hundreds of thousands or even millions of DNA sequences or RNA transcripts. While this is impressive, increasingly sophisticated analysis tools have been required to convert gene array data into gene expression levels. Despite the assumption that noise levels are low, since the number of measurements for an individual gene is small, identifying which signals are affected by noise is a priority. High-density oligonucleotide array (HDONAs) from NCBI GEO shows that, even in the best Human GeneChips 1/4 percent of data are affected by spatial noise. Earlier designs are noisier and spatial defects may affect more than 25 percent of probes. BioConductor R code is available as supplementary material which can be found on the Computer Society Digital Library at http://doi.ieeecomputersociety.org/10.1109/TCBB.2008.108 and via http://bioinformatics.essex.ac.uk/users/wlangdon/TCBB-2007-11-0161.tar.gz. © 2006 IEEE.

Item Type: Article
Subjects: Q Science > QA Mathematics
Q Science > QH Natural history > QH301 Biology
Q Science > QH Natural history > QH426 Genetics
Divisions: Faculty of Science and Health > Mathematical Sciences, Department of
Depositing User: Jim Jamieson
Date Deposited: 29 Sep 2011 15:01
Last Modified: 23 Jan 2019 00:17
URI: http://repository.essex.ac.uk/id/eprint/826

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