Accurate estimates of microarray target concentration from a simple sequence-independent Langmuir model.

TitleAccurate estimates of microarray target concentration from a simple sequence-independent Langmuir model.
Publication TypeJournal Article
Year of Publication2010
AuthorsGharaibeh RZ, Fodor AA, Gibas CJ
JournalPLoS One
Volume5
Issue12
Paginatione14464
Date Published2010 Dec 30
ISSN1932-6203
KeywordsCalibration, Computational Biology, Databases, Genetic, Gene Expression Profiling, Gene Expression Regulation, Humans, Models, Genetic, Models, Statistical, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Reproducibility of Results, RNA, Messenger
Abstract

<p><b>BACKGROUND: </b>Microarray technology is a commonly used tool for assessing global gene expression. Many models for estimation of target concentration based on observed microarray signal have been proposed, but, in general, these models have been complex and platform-dependent.</p><p><b>PRINCIPAL FINDINGS: </b>We introduce a universal Langmuir model for estimation of absolute target concentration from microarray experiments. We find that this sequence-independent model, characterized by only three free parameters, yields excellent predictions for four microarray platforms, including Affymetrix, Agilent, Illumina and a custom-printed microarray. The model also accurately predicts concentration for the MAQC data sets. This approach significantly reduces the computational complexity of quantitative target concentration estimates.</p><p><b>CONCLUSIONS: </b>Using a simple form of the Langmuir isotherm model, with a minimum of parameters and assumptions, and without explicit modeling of individual probe properties, we were able to recover absolute transcript concentrations with high R(2) on four different array platforms. The results obtained here suggest that with a "spiked-in" concentration series targeting as few as 5-10 genes, reliable estimation of target concentration can be achieved for the entire microarray.</p>

DOI10.1371/journal.pone.0014464
Alternate JournalPLoS ONE
PubMed ID21209932
PubMed Central IDPMC3012684
Grant ListR01 GM072619 / GM / NIGMS NIH HHS / United States
R01GM72619 / GM / NIGMS NIH HHS / United States