dorsal/arxiv
View SchemaEffective affinities in microarray data
| Authors | T. Heim, J. Klein Wolterink, E. Carlon, G. T. Barkema |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0605007 |
| URL | https://arxiv.org/abs/q-bio/0605007 |
| DOI | 10.1088/0953-8984/18/18/S03 |
| Journal | J. Phys.: Condens. Matter 18, S525(2006) |
Abstract
In the past couple of years several studies have shown that hybridization in Affymetrix DNA microarrays can be rather well understood on the basis of simple models of physical chemistry. In the majority of the cases a Langmuir isotherm was used to fit experimental data. Although there is a general consensus about this approach, some discrepancies between different studies are evident. For instance, some authors have fitted the hybridization affinities from the microarray fluorescent intensities, while others used affinities obtained from melting experiments in solution. The former approach yields fitted affinities that at first sight are only partially consistent with solution values. In this paper we show that this discrepancy exists only superficially: a sufficiently complete model provides effective affinities which are fully consistent with those fitted to experimental data. This link provides new insight on the relevant processes underlying the functioning of DNA microarrays.
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"abstract": "In the past couple of years several studies have shown that hybridization in\nAffymetrix DNA microarrays can be rather well understood on the basis of simple\nmodels of physical chemistry. In the majority of the cases a Langmuir isotherm\nwas used to fit experimental data. Although there is a general consensus about\nthis approach, some discrepancies between different studies are evident. For\ninstance, some authors have fitted the hybridization affinities from the\nmicroarray fluorescent intensities, while others used affinities obtained from\nmelting experiments in solution. The former approach yields fitted affinities\nthat at first sight are only partially consistent with solution values. In this\npaper we show that this discrepancy exists only superficially: a sufficiently\ncomplete model provides effective affinities which are fully consistent with\nthose fitted to experimental data. This link provides new insight on the\nrelevant processes underlying the functioning of DNA microarrays.",
"arxiv_id": "q-bio/0605007",
"authors": [
"T. Heim",
"J. Klein Wolterink",
"E. Carlon",
"G. T. Barkema"
],
"categories": [
"q-bio.BM",
"cond-mat.soft",
"physics.chem-ph"
],
"doi": "10.1088/0953-8984/18/18/S03",
"journal_ref": "J. Phys.: Condens. Matter 18, S525(2006)",
"title": "Effective affinities in microarray data",
"url": "https://arxiv.org/abs/q-bio/0605007"
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