  The effect of target molecule depletion from the supernatant solution is
incorporated into a physico-chemical model of hybridisation on oligonucleotide
microarrays. Two possible regimes are identified: local depletion, in which
depletion by a given probe feature only affects that particular probe, and
global depletion, in which all features responding to a given target species
are affected. Examples are given of two existing spike-in data sets
experiencing measurable effects of target depletion. The first of these, from
an experiment by Suzuki et al. using custom built arrays with a broad range of
probe lengths and mismatch positions, is verified to exhibit local and not
global depletion. The second dataset, the well known Affymetrix HGU133a latin
square experiment is shown to be very well explained by a global depletion
model. It is shown that microarray calibrations relying on Langmuir isotherm
models which ignore depletion effects will significantly underestimate specific
target concentrations. It is also shown that a combined analysis of perfect
match and mismatch probe signals in terms of a simple graphical summary, namely
the hook curve method, can discriminate between cases of local and global
depletion.
