title: Model-based analysis of two-color arrays (MA2C).
abstract: A novel normalization method based on the GC content of probes is developed for two-color tiling arrays. The proposed method, together with robust estimates of the model parameters, is shown to perform superbly on published data sets. A robust algorithm for detecting peak regions is also formulated and shown to perform well compared to other approaches. The tools have been implemented as a stand-alone Java program called MA2C, which can display various plots of statistical analysis for quality control.
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA. jssong@jimmy.harvard.edu
authors.forename: Jun S
authors.initials: JS
authors.lastname: Song
authors.forename: W Evan
authors.initials: WE
authors.lastname: Johnson
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: Zhu
authors.forename: Xinmin
authors.initials: X
authors.lastname: Zhang
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Arjun K
authors.initials: AK
authors.lastname: Manrai
authors.forename: Jun S
authors.initials: JS
authors.lastname: Liu
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
authors.forename: X Shirley
authors.initials: XS
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics; D002232:Carbocyanines / Q000032:analysis; D019295:Computational Biology / Q000379:methods*; D005456:Fluorescent Dyes / Q000032:analysis*; D015341:Nucleic Acid Probes / Q000737:chemistry*; D020411:Oligonucleotide Array Sequence Analysis / Q000592:standards*; D012984:Software
chemical_list: D002232:Carbocyanines; D005456:Fluorescent Dyes; D015341:Nucleic Acid Probes; C089187:cyanine dye 3; C085321:cyanine dye 5