  The Affymetrix U95 and U133 Latin Square spike-in datasets are reanalysed,
together with a dataset from a version of the U95 spike-in experiment without a
complex non-specific background. The approach uses a physico-chemical model
which includes the effects the specific and non-specific hybridisation and
probe folding at the microarray surface, target folding and hybridisation in
the bulk RNA target solution, and duplex dissociation during the
post-hybridisatoin washing phase. The model predicts a three parameter
hyperbolic response function that fits well with fluorescence intensity data
from all three datasets. The importance of the various hybridisation and
washing effects in determining each of the three parameters is examined, and
some guidance is given as to how a practical algorithm for determining specific
target concentrations might be developed.

Quantitative Methods;Biomolecules