On Tue, Jun 4, 2013 at 2:02 PM, Thomas H. Hampton <thomas.h.hampton at="" dartmouth.edu=""> wrote: > This looks totally cool. > > Is there a place where one can view the schema of the relational db? Hi, Tom. See the vignette for a diagram and for examples. We obviously also assume some familiarity with SQL. Sean > In any case -- Thanks tons! > > Tom > > > > ________________________________________ > From: seandavi at gmail.com [seandavi at gmail.com] on behalf of Sean Davis [sdavis2 at mail.nih.gov] > Sent: Tuesday, June 04, 2013 1:19 PM > To: Thomas H. Hampton > Cc: bioconductor at r-project.org; Jack zhu > Subject: Re: [BioC] GEOquery and Sample Subsets > > On Tue, Jun 4, 2013 at 1:14 PM, Thomas H. Hampton > <thomas.h.hampton at="" dartmouth.edu=""> wrote: >> Exactly! > > This might help: > > http://www.bioconductor.org/packages/release/bioc/html/GEOmetadb.html > > Let us know if you have questions. > > Sean > > >> Thanks. >> >> ________________________________________ >> From: seandavi at gmail.com [seandavi at gmail.com] on behalf of Sean Davis [sdavis2 at mail.nih.gov] >> Sent: Tuesday, June 04, 2013 12:54 PM >> To: Thomas H. Hampton >> Cc: bioconductor at r-project.org >> Subject: Re: [BioC] GEOquery and Sample Subsets >> >> On Tue, Jun 4, 2013 at 12:38 PM, Thomas H. Hampton >> <thomas.h.hampton at="" dartmouth.edu=""> wrote: >>> I am using to GEOquery to establish sample subsets of GEO data -- that is, I would >>> like to know which samples are replicates. >>> >>> I am doing it something like this: >>> >>> gds505 <- getGEO("GDS505") >>> Columns(gds505) >>> >>>> str(Columns(gds505)) >>> 'data.frame': 17 obs. of 4 variables: >>> $ sample : Factor w/ 17 levels "GSM11805","GSM11814",..: 2 4 5 7 9 10 12 14 16 1 ... >>> $ disease.state: Factor w/ 2 levels "normal","RCC": 2 2 2 2 2 2 2 2 2 1 ... >>> $ individual : Factor w/ 10 levels "001","005","011",..: 6 4 1 2 3 5 8 9 10 6 ... >>> $ description : chr "Value for GSM11814: C035 Renal Clear Cell Carcinoma U133A; src: Trizol... >>> >>> The problem I have is that the getGEO command retrieves a rather large object: >>> >>>> print(object.size(gds505), units="Mb") >>> 12.6 Mb' >>> >>> This takes up a lot of time and bandwidth if you plan to do it for thousands of accessions. >>> >>> Is there a way to retrieve less? >> >> Hi, Tom. Are you saying that you really want just the metadata to >> start; in other words, you just want the sample information without >> the expression values? >> >> Sean >> >> >>> I am happy to use R, BioConductor, bioperl or whatever. >>> >>> Best, >>> >>> Tom >>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor