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?
-Rory
________________________________________
From: Gordon K Smyth [sm...@wehi.edu.au]
Sent: 14 April 2013 04:36
To: Rory Stark
Cc: bioc-devel@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.st...@cruk.cam.ac.uk>
> To: "bioc-devel@r-project.org" <bioc-devel@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
>
______________________________________________________________________
The information in this email is confidential and intend...{{dropped:6}}
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
