hi, does somebody know if the annotation packages for the Affymetrix chips will be updated sometimes? i am using the annotation package hgu133plus2 which was created in march and i wonder if there may be some changes, for example retired UniGene IDs or something like that. I found already a probe set that is annotated to GenBank, but not on UniGene, although there exists a UniGene cluster with this GenBank ID. thanks to all

Jianhua can correct me, but I think they are updated quarterly, so some of the annotation is likely to have changed. Sean On Aug 31, 2004, at 6:21 AM, Dipl.-Ing. Johannes Rainer wrote: > hi, > does somebody know if the annotation packages for the Affymetrix chips > will be > updated sometimes? > i am using the annotation package hgu133plus2 which was created in > march and i > wonder if there may be some changes, for example retired UniGene IDs or > something like that. I found already a probe set that is annotated to > GenBank, > but not on UniGene, although there exists a UniGene cluster with this > GenBank > ID. > thanks to all > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor

>Jianhua can correct me, but I think they are updated quarterly, so some >of the annotation is likely to have changed. Now we have both the release and developmental tracks that work with the release and developmental BioC packages, respectively. Only the developmental track gets updated quartely. To get the devel verion you do: >library(reposTools) >install.packages2(PkgName, develOK = TRUE) > >Sean > >On Aug 31, 2004, at 6:21 AM, Dipl.-Ing. Johannes Rainer wrote: > >> hi, >> does somebody know if the annotation packages for the Affymetrix chips >> will be >> updated sometimes? >> i am using the annotation package hgu133plus2 which was created in >> march and i >> wonder if there may be some changes, for example retired UniGene IDs or >> something like that. I found already a probe set that is annotated to >> GenBank, >> but not on UniGene, although there exists a UniGene cluster with this >> GenBank >> ID. >> thanks to all >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

>This implies that one needs to use development versions of annotate, >GO, etc. to be "compatible"? Just for clarification.... The release BioC packages still work for most part but you have to use the devel version for annotation packages that have experienced structural changes. When there is any change to an annotation package, users will be alerted by our NEWS that is broadcasted weekly through BioC mailing list. > >On Aug 31, 2004, at 8:17 AM, John Zhang wrote: > >> >>> Jianhua can correct me, but I think they are updated quarterly, so >>> some >>> of the annotation is likely to have changed. >> >> Now we have both the release and developmental tracks that work with >> the release >> and developmental BioC packages, respectively. Only the developmental >> track gets >> updated quartely. To get the devel verion you do: >> >>> library(reposTools) >>> install.packages2(PkgName, develOK = TRUE) >> >> >>> >>> Sean >>> >>> On Aug 31, 2004, at 6:21 AM, Dipl.-Ing. Johannes Rainer wrote: >>> >>>> hi, >>>> does somebody know if the annotation packages for the Affymetrix >>>> chips >>>> will be >>>> updated sometimes? >>>> i am using the annotation package hgu133plus2 which was created in >>>> march and i >>>> wonder if there may be some changes, for example retired UniGene IDs >>>> or >>>> something like that. I found already a probe set that is annotated to >>>> GenBank, >>>> but not on UniGene, although there exists a UniGene cluster with this >>>> GenBank >>>> ID. >>>> thanks to all >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> Jianhua Zhang >> Department of Biostatistics >> Dana-Farber Cancer Institute >> 44 Binney Street >> Boston, MA 02115-6084 > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

Hi, We can only maintain two branches (it is not like we have unlimited resources), but given that we release twice a year this should not be a substantial problem. If you use the devel branch, then you should use all of it, all software and data. The devel data packages typically do not work with the release branch of the other software tools (like Biobase, affy or annotate). This project, like many others relies on user contributions (and typically that requires more than just submitting your package, but rather doing some of the basic organizational and other work that does not get so much credit - writing documentation, as some have recently pointed out). If anyone would like to contribute to the project, I am sure that we can help them to set up regular rebuilds of the release arm, but please don't get the idea that we have some enourmous amount of time and manpower that are not being used. Robert On Tue, Aug 31, 2004 at 08:23:00AM -0400, Sean Davis wrote: > This implies that one needs to use development versions of annotate, > GO, etc. to be "compatible"? Just for clarification.... > > On Aug 31, 2004, at 8:17 AM, John Zhang wrote: > > > > >> Jianhua can correct me, but I think they are updated quarterly, so > >> some > >> of the annotation is likely to have changed. > > > > Now we have both the release and developmental tracks that work with > > the release > > and developmental BioC packages, respectively. Only the developmental > > track gets > > updated quartely. To get the devel verion you do: > > > >> library(reposTools) > >> install.packages2(PkgName, develOK = TRUE) > > > > > >> > >> Sean > >> > >> On Aug 31, 2004, at 6:21 AM, Dipl.-Ing. Johannes Rainer wrote: > >> > >>> hi, > >>> does somebody know if the annotation packages for the Affymetrix > >>> chips > >>> will be > >>> updated sometimes? > >>> i am using the annotation package hgu133plus2 which was created in > >>> march and i > >>> wonder if there may be some changes, for example retired UniGene IDs > >>> or > >>> something like that. I found already a probe set that is annotated to > >>> GenBank, > >>> but not on UniGene, although there exists a UniGene cluster with this > >>> GenBank > >>> ID. > >>> thanks to all > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor@stat.math.ethz.ch > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > Jianhua Zhang > > Department of Biostatistics > > Dana-Farber Cancer Institute > > 44 Binney Street > > Boston, MA 02115-6084 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+