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:4}}
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
