Biology – Quantitative Biology – Quantitative Methods
Scientific paper
2007-12-06
Phys. Biol. 5 (2008) 016004
Biology
Quantitative Biology
Quantitative Methods
32 pages, 13 figures, minor amendments
Scientific paper
10.1088/1478-3975/5/1/016004
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.
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