[Bioc-devel] Alert to developers about changes to edgeR

Nicolas Delhomme delhomme at embl.de
Fri Mar 16 16:40:57 CET 2012

Dear Gordon,

Thanks for letting us know!


Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany

On 16 Mar 2012, at 03:40, Gordon K Smyth wrote:

> The deadline for the 2.10 Bioconductor release is very close.  There are a few packages that depend on or suggest edgeR.  This email is to alert developers to changes in edgeR that might potentially break code.  One of the changes below was made only two weeks ago, so I thought it would be worth an email to alert people.
> 1. estimateCommonDisp() and estimateGLMCommonDisp() now return dispersion=NA when there is no replication.  This is to force users to make a decision for themselves about what action to take in this case. This means that any subsequent function that uses the common dispersion will fail when there is no replication.  If you want to reproduce earlier behaviour, you need to explicitly enter dispersion=0 to subsequent functions.
> 2. The column headings in the table returned by exactTest() and glmLRT() have changed.  For example, the column called logConc is now logCPM (log counts-per-million).  If anyone is pulling out columns such as logConc by name, such code might be broken.
> There are lots of other changes since the last release, but the above two are fairly recent and the most likely to break dependent code.
> Best wishes
> Gordon
> ---------------------------------------------
> Professor Gordon K Smyth,
> Bioinformatics Division,
> Walter and Eliza Hall Institute of Medical Research,
> 1G Royal Parade, Parkville, Vic 3052, Australia.
> smyth at wehi.edu.au
> http://www.wehi.edu.au
> http://www.statsci.org/smyth
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