title: Accurate estimates of microarray target concentration from a simple sequence-independent Langmuir model.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America.
authors.forename: Raad Z
authors.initials: RZ
authors.lastname: Gharaibeh
authors.forename: Anthony A
authors.initials: AA
authors.lastname: Fodor
authors.forename: Cynthia J
authors.initials: CJ
authors.lastname: Gibas
mesh_terms: D002138:Calibration; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000378:metabolism; D015203:Reproducibility of Results
chemical_list: D012333:RNA, Messenger