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Activity Number:
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116
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Type:
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Contributed
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Date/Time:
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Monday, August 7, 2006 : 8:30 AM to 10:20 AM
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Sponsor:
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Biometrics Section
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| Abstract - #305585 |
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Title:
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Model-Based Analysis of Tiling-Arrays for ChIP-chip
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Author(s):
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William Evan Johnson*+ and Wei Li and Clifford Meyer and X. Shirley Liu
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Companies:
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Harvard University and Dana Farber Cancer Institute and Dana Farber Cancer Institute and Dana Farber Cancer Institute
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Address:
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73 Marathon Street, Arlington, MA, 02474,
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Keywords:
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tiling microarrays ; transcription factor ; chip-chip ; normalization ; linear model ; false discovery rate
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Abstract:
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We propose an analysis algorithm to reliably detect regions enriched by transcription factor Chromatin ImmunoPrecipitation (ChIP) on Affymetrix tiling arrays (chip). We model the baseline probe behavior using probe sequences and copy number on each array and standardize the probes via this probe model, resulting in a unique single chip simultaneous normalization/background adjustment. A robust scoring function is proposed to score regions for ChIP-enrichment, which allows for p-value and FDR calculations. Our method can detect ChIP-regions from single ChIP samples, multiple ChIP samples, or multiple ChIP samples with controls. The single array ChIP-region detection feature minimizes logistical constraints for labs newly adopting ChIP-chip to test protocols and antibodies or allows established ChIP-chip labs to identify samples with questionable quality that contaminate their data.
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