Analysis of Affymetrix ChIP-chip data using starr and R/Bioconductor

Benedikt Zacher; Phillipp Torkler; Achim Tresch

doi:10.1101/pdb.top110

Analysis of Affymetrix ChIP-chip data using starr and R/Bioconductor

Cold Spring Harb Protoc. 2011 May 1;2011(5):pdb.top110. doi: 10.1101/pdb.top110.

Authors

Benedikt Zacher¹, Phillipp Torkler, Achim Tresch

Affiliation

¹ Department of Biochemistry, Center for Integrated Protein Sciences and Munich Center for Advanced Photonics at the Gene Center, Ludwig-Maximilians-University Munich, Munich, Germany.

PMID: 21536772
DOI: 10.1101/pdb.top110

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromatin Immunoprecipitation / methods*
Chromatin Immunoprecipitation / standards
DNA / metabolism*
DNA-Binding Proteins / metabolism*
Microarray Analysis / methods*
Microarray Analysis / standards
Protein Binding

Substances

DNA-Binding Proteins
DNA