title: Sandcastle: software for revealing latent information in multiple experimental ChIP-chip datasets via a novel normalisation procedure.
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 http://reedlab.cardiff.ac.uk/sandcastle.
authors: Cancer and Genetics Building, Cardiff University, School of Medicine, Heath Park, Cardiff, CF14 4XN, UK.
authors: Mark
authors: M
authors: Bennett
authors: Cancer and Genetics Building, Cardiff University, School of Medicine, Heath Park, Cardiff, CF14 4XN, UK.
authors: Katie Ellen
authors: KE
authors: Evans
authors: Cancer and Genetics Building, Cardiff University, School of Medicine, Heath Park, Cardiff, CF14 4XN, UK.
authors: Shirong
authors: S
authors: Yu
authors: Cancer and Genetics Building, Cardiff University, School of Medicine, Heath Park, Cardiff, CF14 4XN, UK.
authors: Yumin
authors: Y
authors: Teng
authors: Cancer and Genetics Building, Cardiff University, School of Medicine, Heath Park, Cardiff, CF14 4XN, UK.
authors: Richard M
authors: RM
authors: Webster
authors: Cancer and Genetics Building, Cardiff University, School of Medicine, Heath Park, Cardiff, CF14 4XN, UK.
authors: James
authors: J
authors: Powell
authors: Cancer and Genetics Building, Cardiff University, School of Medicine, Heath Park, Cardiff, CF14 4XN, UK.
authors: Raymond
authors: R
authors: Waters
authors: Cancer and Genetics Building, Cardiff University, School of Medicine, Heath Park, Cardiff, CF14 4XN, UK.
authors: Simon H
authors: SH
authors: Reed
mesh_terms: D000465:Algorithms; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D057225:Data Mining / Q000379:methods; D030541:Databases, Genetic; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D015233:Models, Statistical; D010363:Pattern Recognition, Automated / Q000379:methods*; D011381:Programming Languages; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012984:Software