title: Analysis of Affymetrix ChIP-chip data using starr and R/Bioconductor.
abstract: This article provides a flexible workflow for the analysis of chromatin immunoprecipitation data (ChIP-chip) that covers issues from quality control, probe sequence remapping, data preprocessing/normalization, visualization, and high-level analysis like peak finding. It emphasizes the peculiarities of single-color Affymetrix arrays, but it is flexible enough to be also amenable to other array platforms. The article is accompanied by extensive code implementing each of the analysis steps.
authors.affiliation: Department of Biochemistry, Center for Integrated Protein Sciences and Munich Center for Advanced Photonics at the Gene Center, Ludwig-Maximilians-University Munich, Munich, Germany.
authors.forename: Benedikt
authors.initials: B
authors.lastname: Zacher
authors.forename: Phillipp
authors.initials: P
authors.lastname: Torkler
authors.forename: Achim
authors.initials: A
authors.lastname: Tresch
mesh_terms: D047369:Chromatin Immunoprecipitation / Q000379:methods* / Q000592:standards; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D046228:Microarray Analysis / Q000379:methods* / Q000592:standards; D011485:Protein Binding
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA