Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

Journal name:
Nature Protocols
Volume:
8,
Pages:
1765–1786
Year published:
DOI:
doi:10.1038/nprot.2013.099
Published online

Abstract

RNA sequencing (RNA-seq) has been rapidly adopted for the profiling of transcriptomes in many areas of biology, including studies into gene regulation, development and disease. Of particular interest is the discovery of differentially expressed genes across different conditions (e.g., tissues, perturbations) while optionally adjusting for other systematic factors that affect the data-collection process. There are a number of subtle yet crucial aspects of these analyses, such as read counting, appropriate treatment of biological variability, quality control checks and appropriate setup of statistical modeling. Several variations have been presented in the literature, and there is a need for guidance on current best practices. This protocol presents a state-of-the-art computational and statistical RNA-seq differential expression analysis workflow largely based on the free open-source R language and Bioconductor software and, in particular, on two widely used tools, DESeq and edgeR. Hands-on time for typical small experiments (e.g., 4–10 samples) can be <1 h, with computation time <1 d using a standard desktop PC.

At a glance

Figures

  1. Count-based differential expression pipeline for RNA-seq data using edgeR and/or DESeq.
    Figure 1: Count-based differential expression pipeline for RNA-seq data using edgeR and/or DESeq.

    Many steps are common to both tools, whereas the specific commands are different (Step 14). Steps within the edgeR or DESeq differential analysis can follow two paths, depending on whether the experimental design is simple or complex. Alternative entry points to the protocol are shown in orange boxes.

  2. Screenshot of Metadata available from SRA.
    Figure 2: Screenshot of Metadata available from SRA.
  3. Screenshot of reads aligning across exon junctions.
    Figure 3: Screenshot of reads aligning across exon junctions.
  4. Plots of sample relations.
    Figure 4: Plots of sample relations.

    (a) By using a count-specific distance measure, edgeR's plotMDS produces a multidimensional scaling plot showing the relationship between all pairs of samples. (b) DESeq's plotPCA makes a principal component (PC) plot of VST (variance-stabilizing transformation)-transformed count data. CT or CTL, control; KD, knockdown.

  5. Plots of mean-variance relationship and dispersion.
    Figure 5: Plots of mean-variance relationship and dispersion.

    (a) edgeR's plotMeanVar can be used to explore the mean-variance relationship; each dot represents the estimated mean and variance for each gene, with binned variances as well as the trended common dispersion overlaid. (b) edgeR's plotBCV illustrates the relationship of biological coefficient of variation versus mean log CPM. (c) DESeq's plotDispEsts shows the fit of dispersion versus mean. CPM, counts per million.

  6. M ('minus') versus A ('add') plots for RNA-seq data.
    Figure 6: M ('minus') versus A ('add') plots for RNA-seq data.

    (a) edgeR's plotSmear function plots the log-fold change (i.e., the log ratio of normalized expression levels between two experimental conditions) against the log counts per million (CPM). (b) Similarly, DESeq's plotMA displays differential expression (log-fold changes) versus expression strength (log average read count).

  7. Histogram of P values from gene-by-gene statistical tests.
    Figure 7: Histogram of P values from gene-by-gene statistical tests.

Accession codes

Referenced accessions

Gene Expression Omnibus

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Author information

Affiliations

  1. Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

    • Simon Anders &
    • Wolfgang Huber
  2. Department of Statistics, University of Oxford, Oxford, UK.

    • Davis J McCarthy
  3. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.

    • Davis J McCarthy
  4. Bioinformatics Division, Walter and Eliza Hall Institute, Parkville, Victoria, Australia.

    • Yunshun Chen &
    • Gordon K Smyth
  5. Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.

    • Yunshun Chen
  6. Functional Genomics Center UNI ETH, Zurich, Switzerland.

    • Michal Okoniewski
  7. Department of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia.

    • Gordon K Smyth
  8. Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.

    • Mark D Robinson
  9. SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland.

    • Mark D Robinson

Contributions

S.A. and W.H. are authors of the DESeq package. D.J.M., Y.C., G.K.S. and M.D.R. are authors of the edgeR package. S.A., M.O., W.H. and M.D.R. initiated the protocol format on the basis of the ECCB 2012 Workshop. S.A. and M.D.R. wrote the first draft and additions were made from all authors.

Competing financial interests

The authors declare no competing financial interests.

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Supplementary information

Zip files

  1. Supplementary Data (546 KB)

    Archive of files used in the protocol. This file is a compressed archive with the following files: the intermediate COUNT files used, a count table used in the statistical analysis, the metadata table and the original “SraRunInfo” CSV file that was downloaded from the NCBI's SRA.

Additional data