title: Noise factor analysis for cDNA microarrays.
abstract: A microarray-image model is used that takes into account many factors, including spot morphology, signal strength, background fluorescent noise, and shape and surface degradation. The model yields synthetic images whose appearance and quality reflect that of real microarray images. The model is used to link noise factors to the fidelity of signal extraction with respect to a standard image-extraction algorithm. Of particular interest is the identification of the noise factors and their interactions that significantly degrade the ability to accurately detect the true gene-expression signal. This study uses statistical criteria in conjunction with the simulation of various noise conditions to better understand the noise influence on signal extraction for cDNA microarray images. It proposes a paradigm that is implemented in software. It specifically considers certain kinds of noise in the noise model and sets these at certain levels; however, one can choose other types of noise or use different noise levels. In sum, it develops a statistical package that can work in conjunction with the existing image simulation toolbox.
authors.affiliation: Texas A&M University, Department of Electrical Engineering, 111D Zachry, College Station, Texas 77843-3128, USA.
authors.forename: Yoganand
authors.initials: Y
authors.lastname: Balagurunathan
authors.forename: Naisyin
authors.initials: N
authors.lastname: Wang
authors.forename: Edward R
authors.initials: ER
authors.lastname: Dougherty
authors.forename: Danh
authors.initials: D
authors.lastname: Nguyen
authors.forename: Yidong
authors.initials: Y
authors.lastname: Chen
authors.forename: Michael L
authors.initials: ML
authors.lastname: Bittner
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Trent
authors.forename: Raymond
authors.initials: R
authors.lastname: Carroll
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D008856:Microscopy, Fluorescence / Q000379:methods*; D008957:Models, Genetic; D015233:Models, Statistical; D015999:Multivariate Analysis; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012815:Signal Processing, Computer-Assisted; D013269:Stochastic Processes