The Detection of Blur in Affymetrix GeneChips

High correlations were obtained between probes in seemingly unrelated probe sets, following an examination of the data from thousands of Affymetrix GeneChips. Investigation revealed that these unexpected correlations were between probes that were adjacent to high-valued probes. Using carefully selected probes, together with simple linear models, the extent of blur has been measured for each CEL file. The cause is shown to be attributable to poorly performing scanners. Blur can result in the doubling of the values of thousands of probes. This in turn can lead to the doubling of the expression level for hundreds of probe sets. Copyright © 2010 Berkeley Electronic Press.