We propose a novel analysis algorithm MATCh (Model-based Analysis of Tiling-array for ChIP-chip) to reliably detect regions enriched by
transcription factor Chromatin ImmunoPrecipitation (ChIP) on Affymetrix tiling arrays (chip). MATCh models the baseline probe behavior by
considering the 25-mer sequence and copy number of probes on a single tiling array. The correlation between the baseline probe model estimates and the
observed measurements can be as high as 0.72. MATCh standardizes the value of each probe in each tiled array via the probe behavior model, eliminating the need for sample normalization. A novel function is proposed to score genomic regions for ChIP-enrichment which allows robust p-value and false discovery rate calculations. MATCh 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 new labs adopting ChIP-chip to test their protocols and antibodies, and allows established ChIP-chip labs to identify samples with questionable quality that might contaminate their
data. MATCh is developed in open-source Python, and can analyze the tiling array data faster than the Affymetrix scanner can scan these arrays.
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