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

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

Author information

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.

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.

PMID:
21536772
DOI:
10.1101/pdb.top110
[Indexed for MEDLINE]

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