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 [[email protected]] Sent: 14 April 2013 04:36 To: Rory Stark Cc: [email protected] 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 <[email protected]> > To: "[email protected]" <[email protected]> > 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}} _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
