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Table 3 Hook characteristics of HG-U133A and HG-U133plus2 chips hybridized with the same RNA using different probe set definitionsa)

From: "Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures

probe set definition chip-type Optical BG non- specific BG N-binding strength PM/MM- gain (S) PM/MM-gain (N) mean S/N-index mean expression index percent absent probe utilizationd)
   logO logN β α logn <λ> <φ> %N %P
# of probe sets
Affymetrix probe sets b)
total HG- U133A 1.89
± 0.04
1.71
± 0.04
2.70
± 0.04
0.99
± 0.03
0.10
± 0.01
0.61
± 0.03
2.09
± 0.05
34
± 3
100%
22,193
total HG- U133plus2 1.81
± 0.04
1.65
± 0.08
2.75
± 0.07
0.85
± 0.01
0.07
± 0.01
0.57
± 0.03
2.18
± 0.07
50
± 3
100%
54,585
A HG- U133plus2 1.82
± 0.06
1.63
± 0.08
2.76
± 0.07
0.86
± 0.01
0.09
± 0.01
0.65
± 0.05
2.11
± 0.07
29
± 3
41%
22,187
notA HG- U133plus2 1.80
± 0.06
1.67
± 0.09
0.83
± 0.01
0.06
± 0.01
0.45
± 0.03
x 64
± 5
59%
32,308
Customized probe sets c)
Ensemble gene HG- U133A 1.89
± 0.05
1.71
± 0.03
2.77
± 0.02
0.97
± 0.03
0.12
± 0.003
0.56
± 0.03
2.21
± 0.04
23
± 3
68%
11,834
  HG- U133plus2 1.82
± 0.06
1.61
± 0.09
2.74
± 0.07
0.84
± 0.01
0.08
± 0.02
0.56
± 0.05
2.18
± 0.07
21
± 3
48%
17,215
Ensemble transcript HG- U133A 1.88
± 0.05
1.71
± 0.03
2.67
± 0.05
0.95
± 0.03
0.10
± 0.01
0.57
± 0.03
2.10
± 0.05
19
± 1
71%
23,740
  HG- U133plus2 1.81
± 0.06
1.65
± 0.09
2.68
± 0.07
0.79
± 0.11
0.04
± 0.09
0.57
± 0.04
2.08
± 0.07
18
± 11
48%
33,977
Ensemble Exon HG- U133A 1.88
± 0.05
1.69
± 0.04
2.64
± 0.06
-0.97
± 0.02
0.11
± 0.01
0.58
± 0.03
2.06
± 0.06
23
± 3
63%
22,299
  HG- U133plus2 1.81
± 0.06
1.62
± 0.08
2.72
± 0.13
0.84
± 0.01
0.09
± 0.01
0.57
± 0.06
2.15
± 0.15
25
± 5
43%
34,541
Refseq HG- U133A 1.88
± 0.05
1.68
± 0.06
2.64
± 0.07
0.96
± 0.02
0.09
± 0.02
0.60
± 0.05
2.04
± 0.07
17
± 3
72%
17,531
  HG- U133plus2 1.83
± 0.06
1.67
± 0.08
2.65
± 0.12
0.83
± 0.01
0.09
± 0.01
0.61
± 0.05
2.04
± 0.12
27
± 7
48%
25,004
  1. a) Raw intensity data were taken from ref. [10]; human reference RNA has been hybridized onto both chip types in 5 replicates. The data are log-averages/±SE
  2. b) Probe set definition of the manufacturer; total...all probe sets; A/notA...probe sets shared/not shared between the P- and A-chips
  3. c) Customized probe sets were filtered using genomic information provided by Ensemble (gene, transcript or exon related) and Refsequ (see [30]); probe set definitions were downloaded from http://brainarray.mbni.med.umich.edu (version 10) as CDF and probe-sequence files
  4. d) Percent and total number of the probes on the respective chip which are used in the respective analysis. Note that the number of probes per set varies between 4 and more than 30 for the customized sets. The data are taken from http://brainarray.mbni.med.umich.edu