Skip to main content

Table 1 Number of probes, probe sets, probe clusters and genes represented on two popular Affymetrix GeneChip microarrays

From: Correlating measurements across samples improves accuracy of large-scale expression profile experiments

   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%)
  1. 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.