Analysis of Affymetrix ChIP-chip data using starr and R/Bioconductor
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Updated: Jun 2, 2026

Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis
Published on: June 27, 2020
Benedikt Zacher1, Phillipp Torkler, Achim Tresch
1Department of Biochemistry, Center for Integrated Protein Sciences and Munich Center for Advanced Photonics at the Gene Center, Ludwig-Maximilians-University Munich, Munich, Germany.
Introduction:
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.
