Table 2
|
Overview of the hybridization characteristics extracted from the hook-analysis. |
|||
| 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 |
|
a) characteristics refer to the PM-probes; for O, M and σ virtually equal values for PM and MM are obtained b) see the accompanying paper [4] for details c) ranges of typical values are taken from the hook-analyses of more than 500 GeneChip arrays of different type and origin (see [5]) | |||
Binder et al. Algorithms for Molecular Biology 2008 3:11 doi:10.1186/1748-7188-3-11 |
|||