[prev in list] [next in list] [prev in thread] [next in thread] 

List:       bioc-devel
Subject:    Re: [Bioc-devel] Alert to developers about changes to edgeR
From:       Nicolas Delhomme <delhomme () embl ! de>
Date:       2012-03-16 15:40:57
Message-ID: 8411B109-60EC-46F0-A40D-CB584E56E4A1 () embl ! de
[Download RAW message or body]

Dear Gordon,

Thanks for letting us know!

Best,

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme@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@wehi.edu.au
> http://www.wehi.edu.au
> http://www.statsci.org/smyth
> 
> ______________________________________________________________________
> The information in this email is confidential and intend...{{dropped:4}}
> 
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


[prev in list] [next in list] [prev in thread] [next in thread]