PASS (Poisson Approximation for Statistical Significance) is a software that can accurately control the FDR level in ChIP data analysis. The method is designed for detecting transcription factor binding, and may not work well for wide spread signals such as nucleopositioning data. If the data is from ChIP-seq, you need to convert each ChIP-seq value into z-scores before using this program.
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Bioinformatics. 2008 Dec 15;24(24):2825-31. Epub 2008 Oct 25.
Poisson approximation for significance in genome-wide ChIP-chip tiling arrays.