Dear Dr. Gentleman and Dr. Davis, Thank you very much for the informative explanation. It is nice to know that limma is somewhat an (positive) outlier. Regards, Adai On Mon, 2005-02-28 at 04:57 -0800, Robert Gentleman wrote: > Hi, > Bioconductor has a release version (just as R does) and that remains > relatively static through its life, which is typically 6 months. Really > only significant bug fixes are done on the release version and all new > development is done on packages in the devel version. One main > difference is that the devel version of BioC uses the devel version of > R (and not the release version of R), mainly because we are using many > of the new features in R (and in some cases creating them). > You can always access either branch of BioC (or R) but it is a *bad* > idea to mix them and the devel version is just that - under > development, if that suits your needs and capabilities you should use > it, otherwise, the releases are about every six months (and hence the > next one is due in late April/early May - I believe that R has just > decided their release date - and we need to know that before we can do > the next BioC release date). > > All of that said, limma is a bit different and I can only suggest > that you direct specific questions to the maintainer (all packages have > a maintainer who can/should answer such questions). > > Robert > > On Feb 28, 2005, at 4:08 AM, Adaikalavan Ramasamy wrote: > > > * From the authors webpage (http://bioinf.wehi.edu.au/limma/), the > > limma > > package version is 1.8.22 dated 24 February 2005. > > > > * From the BioConductor (Release 1.5) webpage > > http://www.bioconductor.org/repository/release1.5/package/html/ > > limma.html > > the limma package version is 1.8.6 dated 27 October 2004. > > > > Is the above discrepancy of nearly 4 months or 15 minor releases > > intentional ? I noticed considerable change in speed of lmFit() speed > > as > > documented in the changelog for version 1.8.15. > > > > Thank you. > > > > Regards, Adai > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > +------------------------------------------------------------------- ---- > ----------------+ > | Robert Gentleman phone: (206) 667-7700 > | > | Head, Program in Computational Biology fax: (206) 667-1319 | > | Division of Public Health Sciences office: M2-B865 > | > | Fred Hutchinson Cancer Research Center > | > | email: rgentlem@fhcrc.org > | > +------------------------------------------------------------------- ---- > ----------------+ > >

> Date: Mon, 28 Feb 2005 12:08:31 +0000 > From: Adaikalavan Ramasamy <ramasamy@cancer.org.uk> > Subject: [BioC] differing versions of limma > To: BioConductor mailing list <bioconductor@stat.math.ethz.ch> > > * From the authors webpage (http://bioinf.wehi.edu.au/limma/), the limma > package version is 1.8.22 dated 24 February 2005. > > * From the BioConductor (Release 1.5) webpage > http://www.bioconductor.org/repository/release1.5/package/html/limma .html > the limma package version is 1.8.6 dated 27 October 2004. > > Is the above discrepancy of nearly 4 months or 15 minor releases > intentional ? You might read Section 2 of the Limma User's Guide "Installing Limma" where this dicrepancy is explained. To add a few more general comments, Limma works on an "always in release" programming model. It doesn't usually have a separate "developmental version", rather I only post versions of the package which I think are completely working and dcoumented versions. Bioconductor proper is released only once every 6 months (unless you're a alpha/beta tester for R as well as Bioconductor), but you are permitted, in fact strongly encouaged, to update limma more often. I post limma to the http://bioinf.wehi.edu/limma site and also to CRAN so as to make this more frequent update possible. Gordon > I noticed considerable change in speed of lmFit() speed as > documented in the changelog for version 1.8.15. > > Thank you. > > Regards, Adai