Open Access Method

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

Jun S Song1,2†, W Evan Johnson1,2†, Xiaopeng Zhu3†, Xinmin Zhang4, Wei Li1,2, Arjun K Manrai5, Jun S Liu2,6, Runsheng Chen3 and X Shirley Liu1,2*

Author Affiliations

1 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA

2 Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA

3 Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China

4 NimbleGen Systems, Inc., Science Court, Madison, Wisconsin 53711, USA

5 Department of Physics, Harvard University, Cambridge, MA 02138, USA

6 Department of Statistics, Harvard University, 1 Oxford Street, Cambridge, MA 02138, USA

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Genome Biology 2007, 8:R178 doi:10.1186/gb-2007-8-8-r178

Published: 29 August 2007

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.