[Bioc-devel] Change in edgeR interface in released version...

Gordon K Smyth smyth at wehi.EDU.AU
Sun Apr 14 05:36:10 CEST 2013

Dear Rory,

Sorry, I didn't intend to make this change to the release version.  I 
over-looked it amongst some documentation updates that I did want to make. 
I have fixed the release code (version 3.2.2) so that DGEList() will 
accept a NULL value again for lib.size.

Just a note on terminology.  In edgeR terminology, the "effective library 
size" is the normalized library size, the product lib.size*norm.factors. 
The default value for lib.size is colSums(counts), which is the actual 
total rather than the effective total.

Best wishes

> Date: Wed, 10 Apr 2013 10:54:14 +0000
> From: Rory Stark <Rory.Stark at cruk.cam.ac.uk>
> To: "bioc-devel at r-project.org" <bioc-devel at r-project.org>
> Subject: [Bioc-devel] Change in edgeR interface in released version...
> I noticed that DiffBind had suddenly broken, and the culprit turned out 
> to be a change in the edgeR interface in the released version (3.2.1). 
> In DGEList, libsize can no longer be passed in as NULL to use the 
> effective library size - it either must be missing, or you need to fill 
> in the effective library sizes yourself.
> -R

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