Intensity isotherms and distributions on oligonucleotide microarrays

We describe a physico-chemical model relating measured fluorescence intensities on oligonucleotide microarrays to the underlying specific target concentration in the hybridised solution via a hyperbolic isotherm response function. The model includes various chemical reactions occurring at the microarray surface and in bulk solution during hybridisation, including specific and non-specific hybridisation, and also the effects of probe-target dissociation during the post hybridisation washing phase. We analyse the distribution of fluorescence intensities for a complete microarray in the light of this physico-chemical model. Our results indicate that the majority of signals in a typical microarray experiment, though not those of the highly expressed genes, belong to the low concentration, linear part of the isotherm. Nevertheless, recognising the existence of the asymptotic saturation part of the isotherm is important for interpreting this distribution over the entire intensity range.