Conrad J Burden 2008 Phys. Biol. 5 016004 doi:10.1088/1478-3975/5/1/016004
Understanding the physics of oligonucleotide microarrays: the Affymetrix spike-in data reanalysed
Conrad J Burden
Show affiliationsThe 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 of the specific and non-specific hybridization and probe folding at the microarray surface, target folding and hybridization in the bulk RNA target solution and duplex dissociation during the post-hybridization washing phase. The model predicts a three-parameter hyperbolic response function that fits well with fluorescence intensity data from all the three datasets. The importance of the various hybridization 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.
- PACS
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87.80.-y Biophysical techniques (research methods)
- Subjects
- Dates
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Issue 1 (March 2008)
Received 5 December 2007, accepted for publication 6 March 2008
Published 26 March 2008
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Understanding the physics of oligonucleotide microarrays: the Affymetrix spike-in data reanalysed
Conrad J Burden 2008 Phys. Biol. 5 016004
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-
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-
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-
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-
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-
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-
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-
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-
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