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.
We address the problem of detection and correction of spatial flaws in oligonucleotide microarrays. We present two similar procedures, of which one is intended solely for use with replicates and the other has wider applicability. By constructing a set of replicates, with one realistically flawed, we are able to examine the extent to which our procedures are capable of repairing the flaw. We find that, for this purpose, our procedures are superior to the existing `Harshlight' procedure.