Table 1
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Notations |
|
| Superscripts |
Assigns main symbols to... |
| P = PM, MM |
Probe type |
| h = N, S |
Non-specific or specific hybridization |
|
|
|
| Subscripts |
Assigns main symbols to... |
| p, c, set |
Probe-, chip- or probe-set-level |
| 0 |
Values after sequence correction |
|
|
|
| Main symbols |
|
 , Mc, Oc |
Probe intensity, maximum intensity upon saturation and optical background |
 ,  |
Linearized (de-saturated) intensities |
| Sset, Nc |
Specific and non-specific signals |
 ,  ,  |
Probe occupancy: total and due to specific and non-specific hybridization |
| xpP,S, xpP,N |
Fraction of specific and of non-specific transcripts among the total amount of bound transcripts |
 ,  ,  |
Binding strength: total and due to specific and non-specific hybridization |
| [S]p, [N]c |
Concentration of specific and non-specific transcript |
 ,  |
Binding constants of a probe for specific and non-specific transcripts |
| s, n |
PM/MM-sensitivity gain for specific and non-specific binding |
| R |
S/N-ratio |
| Δ, Σ |
Hook coordinates |
| Δstart, Σstart |
Starting values of the hook coordinates |
| Δ(0), Σ(0) |
|
| Δ(∞), Σ(∞) |
End values of the hook coordinates |
| α, β |
Vertical and horizontal dimensions of the hook curve |
| DSp |
Discrimination score |
 (Bp) |
Contribution of middle base B to the signal |
 (bm) |
Positional dependent sensitivity propfile; k is the start position of sequence motiv bm which consists of m adjacent nucleotides |
 |
Sequence specific contribution to the intensity |
 |
Sensitivity |
 ,  |
Density distributions of the non-specific and specific signals |
| μP, σP, ρ |
Mean value, standard deviation and coefficient of PM/MM-correlation of the normal distributions of the non-specific background signals |
| λ, λΣ |
decay lengths of the exponential distribution (referring to the S/N-ratio and to the Σ-signal) |
| φc |
Mean specific signal |
|
|
|
| Operation |
|
| g log(x) |
Generalized logarithm |
| <...> |
Arithmetic mean |
Binder and Preibisch Algorithms for Molecular Biology 2008 3:12 doi:10.1186/1748-7188-3-12 |
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