title: A nonlinear mixed-effects model for estimating calibration intervals for unknown concentrations in two-color microarray data with spike-ins.
abstract: In this study, we propose a calibration method for preprocessing spiked-in microarray experiments based on nonlinear mixed-effects models. This method uses a spike-in calibration curve to estimate normalized absolute expression values. Moreover, using the asymptotic properties of the calibration estimate, 100(1-alpha)% confidence intervals for the estimated expression values can be constructed. Simulations are used to show that the approximations on which the construction of the confidence intervals are based are sufficiently accurate to reach the desired coverage probabilities. We illustrate applicability of our method, by estimating the normalized absolute expression values together with the corresponding confidence intervals for two publicly available cDNA microarray experiments (Hilson et al., 2004; Smets et al., 2008). This method can easily be adapted to preprocess one-color oligonucleotide microarray data with a slight adjustment to the mixed model.
authors.affiliation: Catholic University of Leuven and University of Hasselt. pushpike@med.kuleuven.be
authors.forename: Pushpike J
authors.initials: PJ
authors.lastname: Thilakarathne
authors.forename: Geert
authors.initials: G
authors.lastname: Verbeke
authors.forename: Kristof
authors.initials: K
authors.lastname: Engelen
authors.forename: Kathleen
authors.initials: K
authors.lastname: Marchal
mesh_terms: D017360:Arabidopsis; D002138:Calibration; D003116:Color; D004396:Coloring Agents; D003198:Computer Simulation; D016001:Confidence Intervals; D016013:Likelihood Functions; D017711:Nonlinear Dynamics; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data*; D012441:Saccharomyces cerevisiae
chemical_list: D004396:Coloring Agents