* 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.h tml 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

Adai, I think the release packages become static (in terms of version) after a bioconductor release has been made. You can visit the developer package page to get most recent versions of bioconductor packages. As for limma, I'm not sure how quickly the versions make it to the development page, but I don't think it is typically more than a minor release or two behind. Gordon Smyth (much to everyone's benefit--thanks Gordon) is seemingly continually developing new functionality.... Sean ----- Original Message ----- From: "Adaikalavan Ramasamy" <ramasamy@cancer.org.uk> To: "BioConductor mailing list" <bioconductor@stat.math.ethz.ch> Sent: Monday, February 28, 2005 7:08 AM Subject: [BioC] differing versions of limma >* 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 >

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 | +--------------------------------------------------------------------- -- ----------------+