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

[Dick Beyer]

Please ignore my last request.  The solution was pretty straighforward, after a peek at the entity-relationship diagram.

sql <- paste("SELECT DISTINCT gse.gse, gse.title, gse_gsm.gsm, gsm.title",
"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 = " ")

Thanks,
Dick
*******************************************************************************
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
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
http://staff.washington.edu/~dbeyer
*******************************************************************************

On Wed, 16 Dec 2009, Dick Beyer wrote:

> 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,
> Dick
> *******************************************************************************
> 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
> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
> http://staff.washington.edu/~dbeyer
> *******************************************************************************
>
>
>
>