Abstract
High density oligonucleotide microarrays have been one of the most useful techniques which widely used in genomic science. GCRMA is designed to measure the gene expression on the microarrays, which uses a very simple global estimator for the optical noise, and we suggest correcting the optical noise in another location-specific manner in this study. We found the base-effects estimated by location specific optical adjusted data are stronger than those by global optical adjusted data, and there is a little improvement in accuracy for several spike-in probe sets on the used Affymetrix array.