On Thu, Feb 3, 2011 at 3:12 PM, Pan Du <dupan@northwestern.edu> wrote: > Thanks! Sean > I found the gpl table in the GEOmetadb.sqlite database has already included > all information of GEO platforms. So adding a function of matching GPL ID > in > GEOmetadb will be helpful for users not familiar with SQL. The input > parameter can include manufacturer, organism, data_row_count and other chip > information. How do you think? > > Hi, Pan and Denise. A simple convenience function, getBiocPlatformMap(), has been added to the devel version of GEOmetadb that will pull back all (or a subset) of bioconductor platforms known to GEOmetadb and their associated GEO platform information. Sean > > Pan > > > On 2/3/11 10:43 AM, "Sean Davis" <sdavis2@mail.nih.gov> wrote: > > > And we can add those to the GEOmetadb mappings if we have an up- to-date > > list. This goes for other bioconductor annotation packages, as well; > just > > send the data. We stopped trying to keep up, but if given the info, it > is > > straightforward to add those mappings. The GEOmetadb information is > updated > > approximately weekly at this point, I believe. > > > > Sean > > > > On Thu, Feb 3, 2011 at 11:26 AM, Pan Du <dupan@northwestern.edu> wrote: > > > >> Hi Denise > >> > >> Thanks for your suggestion. I agree it will be help to include GEO GPL > IDs > >> for different Illumina chips in the IlluminaIDMapping annotation > package. > >> If > >> you have the mapping available, could you send me the list? So I don't > need > >> to search again. I will add an additional table for this in the > IDMapping > >> packages together with a retrieve function in the lumi package in the > next > >> Bioc release. > >> Thanks! > >> > >> > >> Pan > >> > >> > >> On 2/2/11 4:10 PM, "Denise Mauldin" <dmauldin@systemsbiology.org> > wrote: > >> > >>> Hello, > >>> > >>> I've been using the lumiHuman/Mouse/RatIDMapping packages from > >> Bioconductor > >>> for awhile now. Thanks very much for creating them. I was wondering > if > >> it > >>> would be possible to either add a list of GEO GPL IDs to the package > >> somehow > >>> or if you could send me a corresponding list. By searching through the > >> GEO > >>> GPL records, I think I've figured out that HumanRef8_V3_0_R0_11282963_A > >> is > >>> GPL6883 and I could do this for the remainder of the packages, but I > was > >>> hoping that you may have a list available. > >>> > >>> Thanks, > >>> Denise > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@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@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]