Model-based analysis of tiling-arrays for ChIP-chip.

@article{Johnson2006ModelbasedAO,
  title={Model-based analysis of tiling-arrays for ChIP-chip.},
  author={Welkin E Johnson and Wei Li and Clifford A. Meyer and Raphael Gottardo and Jason S. Carroll and Myles Brown and Xiaole Shirley Liu},
  journal={Proceedings of the National Academy of Sciences of the United States of America},
  year={2006},
  volume={103 33},
  pages={12457-62}
}
We propose a fast and powerful analysis algorithm, titled Model-based Analysis of Tiling-arrays (MAT), to reliably detect regions enriched by transcription factor chromatin immunoprecipitation (ChIP) on Affymetrix tiling arrays (ChIP-chip). MAT models the baseline probe behavior by considering probe sequence and copy number on each array. It standardizes the probe value through the probe model, eliminating the need for sample normalization. MAT uses an innovative function to score regions for… CONTINUE READING
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