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) + 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 + 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 |