Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays. Export

@article{hekstra03, abstract = {Oligonucleotide microarrays are based on the hybridization of labeled mRNA molecules to short length oligonucleotide probes on a glass surface. Two effects have been shown to affect the raw data: the sequence dependence of the probe hybridization properties and the chemical saturation resulting from surface adsorption processes. We address both issues simultaneously using a physically motivated hybridization model. Based on publicly available calibration data sets, we show that Langmuir adsorption accurately describes GeneChip hybridization, with model parameters that we predict from the sequence composition of the probes. Because these parameters have physical units, we are able to estimate absolute mRNA concentrations in picomolar. Additionally, by accounting for chemical saturation, we substantially reduce the compressive bias of differential expression estimates that normally occurs toward high concentrations.}, address = {Center for Studies in Physics and Biology, Laboratory of Mathematical Physics, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.}, author = {Hekstra, D. and Taussig, A. R. and Magnasco, M. and Naef, F.}, citeulike-article-id = {2529653}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/12655013}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=12655013}, day = {1}, issn = {1362-4962}, journal = {Nucleic Acids Res}, keywords = {affy, bg, transcriptomic}, month = {April}, number = {7}, pages = {1962--1968}, posted-at = {2008-03-13 21:57:46}, priority = {2}, title = {Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/12655013}, volume = {31}, year = {2003} }

TY - JOUR ID - hekstra03 L3 - citeulike-article-id:2529653 N2 - Oligonucleotide microarrays are based on the hybridization of labeled mRNA molecules to short length oligonucleotide probes on a glass surface. Two effects have been shown to affect the raw data: the sequence dependence of the probe hybridization properties and the chemical saturation resulting from surface adsorption processes. We address both issues simultaneously using a physically motivated hybridization model. Based on publicly available calibration data sets, we show that Langmuir adsorption accurately describes GeneChip hybridization, with model parameters that we predict from the sequence composition of the probes. Because these parameters have physical units, we are able to estimate absolute mRNA concentrations in picomolar. Additionally, by accounting for chemical saturation, we substantially reduce the compressive bias of differential expression estimates that normally occurs toward high concentrations. IS - 7 JF - Nucleic Acids Res SN - 1362-4962 AD - Center for Studies in Physics and Biology, Laboratory of Mathematical Physics, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA. EP - 1968 TI - Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays. VL - 31 SP - 1962 KW - affy KW - bg KW - transcriptomic AU - Hekstra, D AU - Taussig, AR AU - Magnasco, M AU - Naef, F PY - 2003/04/01/ UR - http://view.ncbi.nlm.nih.gov/pubmed/12655013 ER -