Spatial Defects in 5896 HG-U133A GeneChips

Motivation: 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. Results: 5896 raw data (Affymetrix CEL) files were obtained from ftp:// ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/TABM/E-TABM-185/ Each CEL file was checked for spatial errors. In HG-U133A high-density oligonucleotide array (HDONAs) the mean error rate is only 1.6% which is amongst the best for human GeneChips. However some locations are much more error prone than others, with up to 28% of probes being affected. Removal of erroneous data improves breast cancer survival prediction.