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The effect of target molecule depletion from the supernatant solution isincorporated into a physico-chemical model of hybridisation on oligonucleotidemicroarrays. Two possible regimes are identified: local depletion, in whichdepletion by a given probe feature only affects that particular probe, andglobal depletion, in which all features responding to a given target speciesare affected. Examples are given of two existing spike-in data setsexperiencing measurable effects of target depletion. The first of these, froman experiment by Suzuki et al. using custom built arrays with a broad range ofprobe lengths and mismatch positions, is verified to exhibit local and notglobal depletion. The second dataset, the well known Affymetrix HGU133a latinsquare experiment is shown to be very well explained by a global depletionmodel. It is shown that microarray calibrations relying on Langmuir isothermmodels which ignore depletion effects will significantly underestimate specifictarget concentrations. It is also shown that a combined analysis of perfectmatch and mismatch probe signals in terms of a simple graphical summary, namelythe hook curve method, can discriminate between cases of local and globaldepletion.

Physico-chemical modelling of target depletion during hybridisation on oligonulceotide microarrays