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.