Model-based analysis of two-color arrays (MA2C).
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.
Song
Jun S
JS
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA. jssong@jimmy.harvard.edu
Johnson
W Evan
WE
Zhu
Xiaopeng
X
Zhang
Xinmin
X
Li
Wei
W
Manrai
Arjun K
AK
Liu
Jun S
JS
Chen
Runsheng
R
Liu
X Shirley
XS
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
D002232:Carbocyanines; D005456:Fluorescent Dyes; D015341:Nucleic Acid Probes; C089187:cyanine dye 3; C085321:cyanine dye 5