MAT build 3
MAT (Model-based Analysis of Tiling-array) 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 ChIP enrichment, which allows robust P value and false discovery rate calculations. MAT can detect ChIP regions from a single ChIP sample, multiple ChIP samples, or multiple ChIP samples with controls with increasing accuracy. The single-array ChIP region detection feature minimizes the time and monetary costs for laboratories newly adopting ChIP-chip to test their protocols and antibodies and allows established ChIP-chip laboratories to identify samples with questionable quality that might contaminate their data.
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Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M and Liu XS:
Model-based analysis of tiling-arrays for ChIP-chip.
Proc. Natl. Acad. Sci. USA 103 (2006) 12457-12462.