[BioC] how to get number of samples from GSE with GEOquery

Dick Beyer dbeyer at u.washington.edu
Thu Dec 17 00:24:34 CET 2009

Would someone please tell me if there is a way to get the number of samples, GSMs associated with a GSE, from doing a GEOquery that returns GSEs?  Specifically, I have this query:

sql <- paste("SELECT DISTINCT gse.gse, gse.title, gse.overall_design, gse.repeats, gse.repeats_sample_list, gse.variable, gse.variable_description, gse.supplementary_file, gse.summary",
"FROM", " gsm JOIN gse_gsm ON gsm.gsm=gse_gsm.gsm",
" JOIN gse ON gse_gsm.gse=gse.gse", " JOIN gse_gpl ON gse_gpl.gse=gse.gse",
" JOIN gpl ON gse_gpl.gpl=gpl.gpl", "WHERE",
#" gsm.molecule_ch1 like '%total RNA%' AND",
" gse.title LIKE '%colorectal cancer%' AND",
" gpl.organism LIKE '%Homo sapiens%'",
sep = " ")

So I am getting all the fields I can (I think) for the GSE entries, but I don't see how to get the number of samples for each GSE.  I see from the GEOquery documentation that I could ue getGEO(), but I don't want to get all the samples, I just want to know their names and how many.

If I use the ncbi website (http://www.ncbi.nlm.nih.gov/sites/entrez) and do a GEO DataSets query for a particular GSE, then the number of samples and their names shows up in the browser.

Any help or ideas will be greatly appreciated.

Thanks very much,
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099

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