BioC 2012

Practical workshop

Here are some resources for the edgeR practical workshop presented at BioC 2012, 24-25 July, Fred Hutchinson Cancer Research Center, Seattle, WA.

The practical session consists of two parts:
  1. a brief talk giving an overview of the methods implemented in edgeR (30 mins)
  2. a practical session designed to introduce people to using edgeR for themselves (90 mins)
All of the workshop materials - including presentation slides, the practical worksheet(s) and example dataset - can be downloaded from this page.

Overview talk

The practical session begins with a brief overview talk, designed to introduce the key concepts underpinning analysis of RNA-Seq data with edgeR. This may be a useful recap for people who have used edgeR before.

Topics covered include:
  • biological variability
  • the quadratic mean-variance relationship in RNA-Seq count data
  • variance modelling for RNA-Seq data in edgeR
  • gene-specific variability
We hope that this will provide a good basis for understanding the edgeR functions for conducting differential expression analysis with edgeR in practice.

Those interested can access the talk slides (pdf).

Hands-on session

The bulk of the practical session is devoted to applying edgeR in a case-study of real RNA-Seq data analysis. Users can undertake the analysis themselves and thus gain practical experience of using edgeR. All necessary instructions and advice are in the appropriate version of the practical worksheet. 

In order to complete the case-study, users must be running the statistical software R (preferably the latest version, 2.15.1 at the time of writing). The edgeR package must installed in R and the dataset arab.Rdata must also be available. There are instructions to guide installation in the practical worksheets. 

Note: all users at BioC 2012 running the workshop on an Amazon Web Services virtual machine will be using the development version of edgeR and should therefore use the devel version of the worksheet below.

For conducting the case-study there are two different worksheets and your choice of which to use depends on which version of edgeR you are using.
  • Development version (2.7.31): users familiar with Bioconductor and edgeR may prefer to use the development version of edgeR (version 2.7.31 at the time of writing). This version of the package features the very latest additions and improvements, but is still under active development so will not necessarily be completely stable. However, this current version has been tested and appears (at least for the authors of the package) to be working well. The development version will become the next release version of the package in the next Bioconductor release (October 2012). Users wanting the latest features and to familiarise themselves with new syntax and functions before the next release should use the development version. Here is the edgeR development version of the worksheet (pdf).
  • Release version (2.6.9): less experienced users will probably be using the release version of edgeR, which is version 2.6.9 at the time of writing. This is the current stable version of the edgeR package and will be installed when using the usual Bioconductor procedure for installing packages. If you are in doubt you are probably using (and probably want to use) the release version. Here is the edgeR release version of the worksheet (pdf).
This should provide all that you need to start analysing differential expression in real RNA-Seq data using edgeR!

Davis McCarthy,
Jul 22, 2012, 9:50 AM
Davis McCarthy,
Jul 11, 2012, 4:53 AM
Davis McCarthy,
Jul 11, 2012, 4:44 AM
Davis McCarthy,
Jun 27, 2012, 7:45 AM