Binder, Hans; Krohn, Knut; Preibisch, Stephan

doi:10.1186/1748-7188-3-11

Algorithms for Molecular Biology

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

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 utilization^d)
		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

^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
^b) Probe set definition of the manufacturer; total...all probe sets; A/notA...probe sets shared/not shared between the P- and A-chips
^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
^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

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ISSN: 1748-7188

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