Table 3.

Numbers of probe sets included into the comparisons

Data set	Array comparison	Best match pairs	GeneID pairs	Multiple original sets (%)	Multiple verified sets (%)
hESC	HG-U133A vs. HG-U133Plus2.0	—	12661	36.7	32.2
mCPI	MG-U74Av2 vs. MOE430 2.0	8595	7735	26.4	14.9
ALL, IM	HG-U95Av2 vs. HG-U133A	8429	8240	25.2	18.9

The best match pairs provided by Affymetrix are based on the similarity of the target sequences of the probe sets. The GeneID pairs were obtained by assigning the probe sets to GeneID identifiers. Only GeneIDs for which probes existed on original, verified and alternative probe sets were considered. If multiple probe sets corresponded to the same GeneID, their values were averaged. The last two columns show the proportion of GeneIDs with multiple probe sets when GeneID pairs of original and verified probe sets were formed.