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
Gordon
> 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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