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Publication Detail
A Survey of Spatial Defects in Homo Sapiens Affymetrix GeneChips
Abstract
Modern biology has moved from a science of individual measurements to a science where data are collected on an industrial scale. Foremost amongst 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. Whilst 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 1/4percent of data are affected by spatial noise. Earlier designs are more noisy and spatial defects may affect more than 25percent of probes. BioConductor R code is available as supplementary material and via \hrefhttp://bioinformatics.essex.ac.uk/users/wlangdon/TCBB-2007-11-0161.tar.gzhttp://bioinformatics.essex.ac.uk/users/wlangdon/TCBB-2007-11-0161.tar.gz
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