[BioC] Adding Illumina GEO GPL IDs to IlluminaIDMapping?

[Pan Du]

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
>> 
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