Pixel-level signal modelling with spatial correlation for two-colour microarrays.

Statistical models for spot shapes and signal intensities are used in image analysis of laser scans of microarrays. Most models have essentially been based on the assumption of independent pixel intensity values, but models that allow for spatial correlation among neighbouring pixels can accommodate errors in the microarray slide and should improve the model fit. Five spatial correlation structures, exponential, Gaussian, linear, rational quadratic and spherical, are compared for a dataset with 50-mer two-colour oligonucleotide microarrays and 452 probes for selected Arabidopsis genes.