The practical session consists of two parts:
All of the workshop materials - including presentation slides, the practical worksheet(s) and example dataset - can be downloaded from this page.
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:
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).
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.
This should provide all that you need to start analysing differential expression in real RNA-Seq data using edgeR!
Teaching Materials >