Model-based Analysis of 2-Color Arrays

MA2C

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. Upon changing the file format, the program also works on Agilent data.

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Track Vervion

Converted Agilent Data Example

Reference:
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