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1: Genome Biol. 2007;8(8):R178.Click here to read Click here to read Links

Model-based analysis of two-color arrays (MA2C).

Song JS, Johnson WE, Zhu X, Zhang X, Li W, Manrai AK, Liu JS, Chen R, Liu XS.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA. jssong@jimmy.harvard.edu

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.

PMID: 17727723 [PubMed - indexed for MEDLINE]

PMCID: PMC2375008