Table 1.

Summary statistics for array designs studied, comparing two annotation methods

Array	Probes or probe sets	Probes for ‘known’ genesb	Known genes assayed	Unassigned probesb	Probes/gene (average)
Illumina (Mfg)a	24 114	17 143	14 420	6971	1.19
Illumina (BLAT)		19 924	16 847	2978c	1.18
Affymetrix (Mfg)	54 675	34 089	16 610	20 586d	2.05
Affymetrix (BLAT)		33 922	18 417	20 600c	1.84

^aMfg, Manufacturer's annotations; BLAT, our own annotations computed using BLAT alignments to the genomic sequence.

^b‘Known genes’ are genes identified in the GoldenPath ‘refGene’ or ‘knownGene’ tables, including transcript information from the ‘all_mrna’ table to determine exon overlaps. We designate all other potential transcripts ‘unassigned probes’.

^cIncludes probes not yielding BLAT results.

^dIncludes 14 334 probes where no gene name is listed by the manufacturer.