[BioC] GEOquery question -- suppressing download for GPL queries?

[Sean Davis]

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
> list.

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.

library(GEOmetadb)
# 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
gplInfo[82:86,]

     gpl                                                    title
organism manufacturer
82 GPL92         Affymetrix GeneChip Human Genome U95 Set HG-U95B Homo
sapiens   Affymetrix
83 GPL93         Affymetrix GeneChip Human Genome U95 Set HG-U95C Homo
sapiens   Affymetrix
84 GPL94         Affymetrix GeneChip Human Genome U95 Set HG-U95D Homo
sapiens   Affymetrix
85 GPL95         Affymetrix GeneChip Human Genome U95 Set HG-U95E Homo
sapiens   Affymetrix
86 GPL96 Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Homo
sapiens   Affymetrix


> 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.

Sean