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

doi:10.1186/gb-2007-8-8-r178

Genome Biology

Volume 8
Issue 8

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Liu XS

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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

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

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

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

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

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

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

author email corresponding author email* Contributed equally

Genome Biology 2007, 8:R178doi:10.1186/gb-2007-8-8-r178


Published:	29 August 2007

Subject areas: Bioinformatics, Genome studies, Genetics

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.