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Sandcastle: software for revealing latent information in multiple experimental ChIP-chip datasets via a novel normalisation procedure

Bennett, Mark Richard, Evans, Katie Ellen, Yu, Shirong, Teng, Yumin, Webster, Richard, Powell, James, Waters, Raymond and Reed, Simon Huw 2015. Sandcastle: software for revealing latent information in multiple experimental ChIP-chip datasets via a novel normalisation procedure. Scientific Reports 5 , 13395. 10.1038/srep13395

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Abstract

ChIP-chip is a microarray based technology for determining the genomic locations of chromatin bound factors of interest, such as proteins. Standard ChIP-chip analyses employ peak detection methodologies to generate lists of genomic binding sites. No previously published method exists to enable comparative analyses of enrichment levels derived from datasets examining different experimental conditions. This restricts the use of the technology to binary comparisons of presence or absence of features between datasets. Here we present the R package Sandcastle — Software for the Analysis and Normalisation of Data from ChIP-chip AssayS of Two or more Linked Experiments — which allows for comparative analyses of data from multiple experiments by normalising all datasets to a common background. Relative changes in binding levels between experimental datasets can thus be determined, enabling the extraction of latent information from ChIP-chip experiments. Novel enrichment detection and peak calling algorithms are also presented, with a range of graphical tools, which facilitate these analyses. The software and documentation are available for download from

Item Type: Article
Date Type: Publication
Status: Published
Schools: Medicine
Subjects: R Medicine > R Medicine (General)
Publisher: Nature Publishing Group
ISSN: 2045-2322
Date of First Compliant Deposit: 30 March 2016
Date of Acceptance: 24 July 2015
Last Modified: 28 Jun 2019 02:40
URI: http://orca.cf.ac.uk/id/eprint/84173

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