Model-based Analysis of 2-Color Arrays





Jun S. Song, W. Evan Johnson, Xiaopeng Zhu, X. Shirley Liu



Abstract: High-density oligonucleotide tiling-microarrays are currently providing a powerful tool for genome-wide in vivo DNA footprinting assays, yielding unprecedented insights into tissue-specific protein-DNA interactions and chromatin structure.  Despite the impressive advances, however, the technology still suffers from numerous complications caused by background noise and probe-specific effects.  A few computational methods modeling sequence-related probe effects are now available for Affymetrix tiling arrays, but no counterpart is yet available for two-color arrays.


Results: 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.  Accompanying the normalization method, a robust algorithm for detecting peak regions is formulated and also shown to perform well compared to other approaches.  The tools presented herein have been implemented for NimbleGen tiling arrays as a stand-alone Java program, which can also display various plots of statistical analysis for quality control of experiments.


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Contact: at, xsliu at jimmy dot harvard dot edu


Track Vervion

Song J, Johnson WE, Zhu X, Zhang X, Li W, Manrai AK, Liu JS, Chen R and Liu XS: Modelbased analysis for 2-color arrays (MA2C). [ Paper]


Last updated on Sept 23, 2007