Validation of the GeneChip Human Mapping 500(500 K) microarray with the high-density CytoScan HD microarray.
Intensity signals of single nucleotide polymorphisms (SNPs) or non-polymorphic probes are expressed as log2 ratios from chromosomes 3, 4, and 5 of the tumor R496 explored using the 500 K microarray (upper panel) and HD 2.7 microarray (lower panel). In both panels, the y-axis depicts a log2 ratio scale from –1.5 to 1.5, and the x-axis shows the ideogram of the explored chromosomes with genome positions. The horizontal line crossing the point y = 0 corresponds to 2 copies. The average density of explored positions is more than 5 times higher in the HD 2.7 microarray than that in the 500 K microarray (see materials and methods).