2.3. Positional-Dependent Sequence Model and Sequence Effect Size
The intensity of a microarray probe is modeled in dependency of specific/non-specific target concentration, saturation intensity and a sequence effect δA as described in [27]. We employ a positional-dependent nearest neighbor model describing the sequence effect as the sum of sensitivity terms over all 16 dinucleotide subsequences ξk,k+1 ∈ {A, C, G, T}2 and all positions k = 1...24 of the 25-meric probe sequence ξ [17] (1) δA(ξ)=∑K=124σk(ξk,k+1) The sensitivity profiles were calculated using the non-specific hybridization signal of all PM probes of the arrays (see Supplemental Figure S2 for an example).
We define the maximum sensitivity amplitude as the maximum difference between all pairs of NN-sensitivity profiles (2) log(Kdiff)≡δAmax all ξ−δAmin all ξ of the non-specific hybridization mode. It determines how much (in units of log intensity contributions) a probe could shine brighter than another one given that both probes target the same transcript and thus it estimates the sequence effect size.