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Table 2 Overview of the hybridization characteristics extracted from the hook-analysis.

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

Characteristics Equationb) characterizes...b) Typical rangec)
Chip-level(index "c" is omitted)
Optical background, Oa) log O = log O zones ...residual background intensity not related to hybridization; it is obtained using the Affy-zone algorithm performed prior to hook analysis 1.4 – 2.0
N-background signala) log N = Σ(0) + 1 2 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaqcfa4aaSaaaeaacqaIXaqmaeaacqaIYaGmaaaaaa@2E55@ Δ(0) ... mean background PM-intensity due to N-hybridization 1.0 – 2.5
PM/MM-gain in the N- range log n = Δ(0) ...the PM-over-MM excess of the intensity presumably due to a certain amount of weakly (S-) expressed transcripts in the N-range 0.0 – 0.15
Saturation signala) log M = Σ(∞) ... the maximum possible intensity of the spots 4.0 – 4.9
N-binding strengtha) log XN≡ log XPM, N= -β + 1 2 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaqcfa4aaSaaaeaacqaIXaqmaeaacqaIYaGmaaaaaa@2E55@ Δ(0) ... the (binding) strength of non- specific hybridization; measuring range of the chip 2.2 – 3.2
PM/MM-gain (S, the PM- over-MM excess of the intensity in the S-range) log s = α - Δ(0) ...the effect of the mismatch on specific binding 0.8 – 1.1
Mean S/N-ratioa) λ = log(R + 1)R > 0.5 ...mean (log-) S/N-ratio; R-range over which the density of expression values decays by one order of magnitude 0.2 – 1.5
Mean expression levela) φ = λ + log XN
S = 10-φ
...mean (log-) expression index in units of the specific binding strength 1.0 – 2.5
Standard deviation of the N- distributiona) σ ...residual scatter of the corrected PM-intensities in the N-range (log- scale) 0.25 – 0.35
Percent non-specific, %N; fraction of N-probes %N, fabsent = %N/100 Percentage of probe sets in the N- range;...amount of "absent" probes 20 – 95%
Probe-set level(index "set" is omitted)
Hook coordinates Σhook, Δhook ...log-mean and log difference of the PM and MM intensities after optical background correction 1 – 4.7 and 0.0 – 1.1
S/N-ratio R ...ratio of the specific binding strength of the probe set and the mean non-specific binding strength of the chip, signal-to-noise level 0 – 100, R = 0 indicates "absent" probes
expression level LS ≡ LPM, S ...expression degree in intensity units (PMonly, MMonly and PM-MM estimates) 10 – 100,000
S-binding strength XS ≡ XPM, S ...specific binding strength obtained as PMonly, MMonly or PM-MM_difference estimate 0 – 1
  1. a) characteristics refer to the PM-probes; for O, M and σ virtually equal values for PM and MM are obtained
  2. b) see the accompanying paper [4] for details
  3. c) ranges of typical values are taken from the hook-analyses of more than 500 GeneChip arrays of different type and origin (see [5])