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Question: Adding Illumina GEO GPL IDs to IlluminaIDMapping?
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gravatar for Pan Du
7.7 years ago by
Pan Du1.2k
Pan Du1.2k 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 at="" 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
ADD COMMENTlink modified 7.7 years ago by Sean Davis21k • written 7.7 years ago by Pan Du1.2k
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gravatar for Sean Davis
7.7 years ago by
Sean Davis21k
United States
Sean Davis21k 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 > [[alternative HTML version deleted]]
ADD COMMENTlink written 7.7 years ago by Sean Davis21k
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? Pan On 2/3/11 10:43 AM, "Sean Davis" <sdavis2 at="" 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 at="" 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 at="" 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 at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >>
ADD REPLYlink written 7.7 years ago by Pan Du1.2k
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]]
ADD REPLYlink written 7.7 years ago by Sean Davis21k
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