Question: GEOquery question -- suppressing download for GPL queries?
gravatar for Sean Davis
9.6 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Tue, Mar 2, 2010 at 12:43 PM, Bill Gibb <bgibb at=""""> 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
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