Spatial effects on oligonucleotide arrays. An example oligonucleotide array showing log-ratios of PM versus geometric mean PM in a yellow-cyan color scale. The omitted MM probes, shown in black, appear as horizontal stripes. (a) Relative PM values after global normalization; (b) results after spatial normalization. (c)The difference (of log(PM)) between the two, representing the spatial bias used for normalization.