[BioC] GEOquery question -- suppressing download for GPL queries?
sdavis2 at mail.nih.gov
Tue Mar 2 19:16:25 CET 2010
On Tue, Mar 2, 2010 at 12:43 PM, Bill Gibb <BGibb at genomichealth.com> wrote:
> Dear Sean,
> I am not sure whether this should be posted to the Bioconductor mailing
I'm posting to the list, as these types of queries are often useful for others.
> I would like to use getGEO(“GPLxxx”) to determine whether a platform given
> by “GPLxxx” exists in the NCBI database (as opposed to downloading the data
> matrix associated with the platform). Checking the mailing list archives, I
> noticed that you have introduced a “quiet=TRUE” option into development. My
> understanding is the “quiet” option allows one to suppress the download
> progress indicators, but does not suppress the download itself.
Your understanding is exactly correct.
> Would there
> also be a way to query GEO to see whether platform GPLxxx exists, without
> downloading the data associated with that platform? Reason: I would like to
> use GEOquery to validate user-supplied platform annotation without having to
> wait for the data matrix download.
Jack Zhu and I produced the GEOmetadb package to deal with situations
like this. It assumes some knowledge of SQL, but not much.
# data stored in a SQLite file updated weekly
# you need do this only once
fname = getSQLiteFile()
con = dbConnect('SQLite',fname)
# run an example query (runs instantaneously, pretty much)
gplInfo = dbGetQuery(con,'select gpl,title,organism,manufacturer from gpl')
# example of results
82 GPL92 Affymetrix GeneChip Human Genome U95 Set HG-U95B Homo
83 GPL93 Affymetrix GeneChip Human Genome U95 Set HG-U95C Homo
84 GPL94 Affymetrix GeneChip Human Genome U95 Set HG-U95D Homo
85 GPL95 Affymetrix GeneChip Human Genome U95 Set HG-U95E Homo
86 GPL96 Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Homo
> Alternatively, is GEO’s table of GPL indices available from NCBI? I couldn’t
> find anything about that on the GEO website.
They do not have indices of the available entities, last I checked.
That was part of the motivation for GEOmetadb.
Let us know if you have further questions or need help with SQL
queries to get what you want.
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