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Stem Cell Transcriptional Networks pp 45–79Cite as

edgeR for Differential RNA-seq and ChIP-seq Analysis: An Application to Stem Cell Biology

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1150))

Abstract

The edgeR package, an R-based tool within the Bioconductor project, offers a flexible statistical framework for detection of changes in abundance based on counts. In this chapter, we illustrate the use of edgeR on a human embryonic stem cell dataset, in particular for RNA-seq and ChIP-seq data. We focus on a step-by-step statistical analysis of differential expression, going from raw data to a list of putative differentially expressed genes and give examples of integrative analysis using the ChIP-seq data. We emphasize data quality spot checks and the use of positive controls throughout the process and give practical recommendations for reproducible research.

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Authors and Affiliations

  1. Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland

    Olga Nikolayeva & Mark D. Robinson

  2. SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland

    Olga Nikolayeva & Mark D. Robinson

Authors
  1. Olga Nikolayeva
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  2. Mark D. Robinson
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Corresponding author

Correspondence to Mark D. Robinson .

Editor information

Editors and Affiliations

  1. Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA

    Benjamin L. Kidder

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Nikolayeva, O., Robinson, M.D. (2014). edgeR for Differential RNA-seq and ChIP-seq Analysis: An Application to Stem Cell Biology. In: Kidder, B. (eds) Stem Cell Transcriptional Networks. Methods in Molecular Biology, vol 1150. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0512-6_3

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  • DOI: https://doi.org/10.1007/978-1-4939-0512-6_3

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-0511-9

  • Online ISBN: 978-1-4939-0512-6

  • eBook Packages: Springer Protocols

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