ArticlePloS one2010
Accurate estimates of microarray target concentration from a simple sequence-independent Langmuir model.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes.BMC genomics · 2019Article
- Single-stranded DNA catalyzes hybridization of PCR-products to microarray capture probes.PloS one · 2014Article
- Probing hybridization parameters from microarray experiments: nearest-neighbor model and beyond.Nucleic acids research · 2012Article
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Authors and funding
3 authors.
Funding
Abstract
backgroundMicroarray 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. PRINCIPAL
findingsWe 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.
conclusionsUsing 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.
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