Table 1

Number of probes, probe sets, probe clusters and genes represented on two popular Affymetrix GeneChip microarrays

Affymetrix

APM

Remap

Cleaner

U95Av2

Probes

200,073

163,939 (82%)

154,485 (77%)

83,862 (42%)

Probe-sets

12,625

9,130 (72%)

8,410 (67%)

6,011 (48%)

EntrezID

8,975

8,781 (98%)

8,410 (94%)

5,923 (66%)

U133plus2

Probes

594,532

326,265 (55%)

318,978 (54%)

153,960 (26%)

Probe-sets

54,675

19,887 (36%)

18,303 (33%)

12,162 (22%)

EntrezID

20,327

18,596 (91%)

18,303 (90%)

11,728 (58%)

We report the number of probes, probe-sets, probe clusters and unique EntrezIDs for the U95av2 and U133plus2 platforms according to Affymetrix, AffyProbeMiner (APM), Remap, and Cleaner annotation. Remap is the first stage of Cleaner, and here it is used to report the number of probes with homology to RefSeq transcripts and the number of probe sets and genes with at least one probe homolog. For simplicity of presentation, we refer to Remap and Cleaner probe clusters as probe sets in this table.

Alvarez et al. Genome Biology 2009 10:R143   doi:10.1186/gb-2009-10-12-r143