Table 1 Notations

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

${\text{I}}_{\text{p}}^{\text{P}}$, M_c, O_c

Probe intensity, maximum intensity upon saturation and optical background

$L_{0,p}^P$, $L_p^{P,h}$

Linearized (de-saturated) intensities

S_set, N_c

Specific and non-specific signals

${\Theta }_{\text{p}}^{\text{P}}$, ${\Theta }_{\text{p}}^{\text{P},\text{S}}$, ${\Theta }_{\text{p}}^{\text{P},\text{N}}$

Probe occupancy: total and due to specific and non-specific hybridization

x_p^P,S, x_p^P,N

Fraction of specific and of non-specific transcripts among the total amount of bound transcripts

${\text{X}}_{\text{p}}^{\text{P}}$, ${\text{X}}_{\text{p}}^{\text{P},\text{S}}$, ${\text{X}}_{\text{p}}^{\text{P},\text{N}}$

Binding strength: total and due to specific and non-specific hybridization

[S]_p, [N]_c

Concentration of specific and non-specific transcript

${\text{K}}_{\text{p}}^{\text{P},\text{S}}$, ${\text{K}}_{\text{p}}^{\text{P},\text{N}}$

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

Δ_start, Σ_start

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

DS _p

Discrimination score

${\epsilon }_{13}^{\text{P},\text{h}}$(B_p)

Contribution of middle base B to the signal

$\delta {\epsilon }_{\text{k}}^{\text{P},\text{h}}$(b_m)

Positional dependent sensitivity propfile; k is the start position of sequence motiv b_m which consists of m adjacent nucleotides

$\delta {\text{A}}_{\text{p}}^{\text{P}}$

Sequence specific contribution to the intensity

${\text{Y}}_{\text{p}}^{\text{P},\text{h}}$

Sensitivity

$p_p^N$, $p_c^S$

Density distributions of the non-specific and specific signals

μ^P, σ^P, ρ

Mean value, standard deviation and coefficient of PM/MM-correlation of the normal distributions of the non-specific background signals

λ, λ_Σ

decay lengths of the exponential distribution (referring to the S/N-ratio and to the Σ-signal)

φ _c

Mean specific signal

Operation

g log(x)

Generalized logarithm

<...>

Arithmetic mean