On 05/14/2013 10:42 AM, Cook, Malcolm wrote: > this is potentially a very important point > > however, the lack of easy install availability of previous versions of bioc packages works against it.... I'm not understanding your comment. Bioc versions are released with specific R versions. Install the appropriate R version, and get the corresponding Bioc packages via biocLite(). Challenges occur when trying to install old R on new hardware (e.g., because the old R doesn't compile with new gcc or new libraries), but that's probably not what you mean? Martin > > ~ malcolm_cook at stowers.org > > ________________________________________ > From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] on behalf of Marc Carlson [mcarlson at fhcrc.org] > Sent: Monday, May 13, 2013 3:45 PM > To: bioconductor at r-project.org > Subject: Re: [BioC] advantages of annotation packages > > Just adding to what Martin already said, it's mostly about making your > research more easily reproducible by using a consistent and traceable > source for your information. This sort of thing is important for doing > science, where other people will need to reproduce your results exactly. > If all you had was your own personal data.frame, nobody else can really > work with that unless you also make it available online etc. And then > assuming you can serve it up somewhere in perpetuity, you also have to > explain exactly how you made it etc. In short, when you went to write > the methods section for your findings, you would end up making and > maintaining your own annotation resource and thus reinventing the wheel. > > There are other advantages too. For example, many different kinds of > annotation data are made into packages together, so you can know which > version of GO was being used by a large group of people and also which > entrez gene IDs were considered valid etc. So things are overall more > standardized for a given version of bioconductor, which can aid in > collaborations (since people are basically all working off the same data > set). > > > Marc > > > > On 05/10/2013 07:03 PM, Martin Morgan wrote: >> On 05/10/2013 01:17 AM, Rameswara Sashi Kiran Challa wrote: >>> Hi All, >>> >>> Could anyone please elucidate advantages of having an Annotation package >>> for an organism or point me to any documentation that clearly lists >>> all the >>> various thoughts behind coming up with an Annotation package. >>> >>> Will not having a data frame in R (with rows as genes and columns as >>> various types of annotations like GO, KEGG, Unigene, etc) suffice? >>> What are >> >> One aspect not mentioned is that one gets to exploit R's packaging >> system to provide easily distributed and documented versions of the >> data. Suppose you created the package eight months ago and have >> forgotten some of the detaiils. Easy, check out the package >> description and help page. Say you're working with a couple of >> colleagues, and you've been relatively disciplined about incrementing >> the annotation package when your data changes (or are using a public >> Bioc annotation package, with versions strictly tied to R / Bioc >> releases). Easily spot when unusual results are due to differences in >> data version (hence the frequent request for the output of >> 'sessionInfo()' on this mailing list) and adopt / instill 'best >> practices' that make sure everyone on the team (including yourself, >> even if your team is only 1) are using the same version. >> >> Martin >> >>> the advantages of having a AnnodbBimap objects and building a >>> package? Are >>> there any technical benefits like faster access of information? >>> >>> Thanks for your time, >>> >>> -Sashi >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793