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

Rory Stark Rory.Stark at cruk.cam.ac.uk
Sun Apr 14 22:17:44 CEST 2013

Hi Gordon-

No problem, the change was easy to spot and fix. I wanted to want anyone else who is depending on this invaluable package.

I do realize that I have been misusing the "effective" library size label, which includes the normalization factors. I wanted to distinguish between providing the total number of sequence reads in the library, including "background" reads, vs. the number of reads in specified intervals (genes, peaks). Any ideas of useful terminology for distinguishing between these two counts?

From: Gordon K Smyth [smyth at wehi.EDU.AU]
Sent: 14 April 2013 04:36
To: Rory Stark
Cc: bioc-devel at r-project.org
Subject: Change in edgeR interface in released version...

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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