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Question: GEOmetadb query
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gravatar for BorisZybailov@gmail.com
7.8 years ago by
Dear list, I installed GEOmetadb in order to find all the human cancer-related gene expression GEO series, for which there are also aCGH data available. But I can not figure out how to do this and I would really appreciate any advice. thank you! Boris > sessionInfo() R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GOstats_2.12.0 RSQLite_0.8-1 DBI_0.2-5 graph_1.24.2 Category_2.12.0 [6] stjudem_1.2.2 macat_1.20.0 annotate_1.24.1 AnnotationDbi_1.8.1 Biobase_2.6.1 loaded via a namespace (and not attached): [1] genefilter_1.28.2 GO.db_2.3.5 GSEABase_1.8.0 RBGL_1.22.0 splines_2.10.1 survival_2.35-7 [7] tools_2.10.1 XML_2.6-0 xtable_1.5-6 [[alternative HTML version deleted]]
ADD COMMENTlink modified 7.8 years ago by Jack Zhu170 • written 7.8 years ago by BorisZybailov@gmail.com10
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gravatar for Sean Davis
7.8 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Thu, Jan 21, 2010 at 11:42 PM, <boriszybailov at="" gmail.com=""> wrote: > Dear list, > > I installed GEOmetadb in order to find all the human cancer-related gene > expression GEO series, > for which there are also aCGH data available. But I can not figure out how > to do this and > I would really appreciate any advice. Hi, Boris. Just to clarify, you want to find human cancer samples with both gene expression and copy number data? Sean
ADD COMMENTlink written 7.8 years ago by Sean Davis21k
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gravatar for Jack Zhu
7.8 years ago by
Jack Zhu170
Jack Zhu170 wrote:
Hi Boris and Sean, I agree that we probably can not directly find human cancer samples with both gene expression and copy number data. In GEO, a gene expression GSM and a copy number GSM are two different entries even molecular of these two samples were extracted from a same human cancer sample. Whether a user can find any clue between these two GSMs will depend on how the submitter submitted the data to GEO. But at GSE level, GEO has introduced Super GSE concept, which tries to put all related GSEs (mightbe different platforms) under one Super GSE for a manuscript (you might want to double check with GEO about this), but I am not sure how many such super GSEs are there. If you try to find out what lab/center submitted both gene expression and copy number data, I would try this (need some reading and manual comparing at the end): > library(GEOmetadb) > getSQLiteFile() > con <- dbConnect(SQLite(), "GEOmetadb.sqlite") #### Find human cancer expression GSMs: > gsm_human_cancer_exp <- sqliteQuickSQL(con,"SELECT DISTINCT gsm FROM gsm WHERE characteristics_ch1 LIKE '%cancer%' AND molecule_ch1 = 'total RNA' AND organism_ch1 = 'Homo sapiens' ") ## Convert to GSE > gse_conversion1 <- geoConvert(gsm_human_cancer_exp[[1]], 'gse') > gse_human_cancer_exp <- unique(gse_conversion1$gse$to_acc) #### Find human cancer aCGH GSMs (might not be accurate): > gsm_human_cancer_cgh <- sqliteQuickSQL(con,"SELECT DISTINCT gsm FROM gsm WHERE characteristics_ch1 LIKE '%cancer%' AND molecule_ch1 = 'genomic DNA' AND organism_ch1 = 'Homo sapiens' ") ## Convert to GSE > gse_conversion2 <- geoConvert(gsm_human_cancer_cgh[[1]], 'gse') > gse_human_cancer_cgh <- unique(gse_conversion2$gse$to_acc) ## Try to compare manually if any GSEs of gse_human_cancer_exp and gse_human_cancer_cgh are from the same submitter, or lab > dbDisconnect(con) Hope this helps. Jack On Thu, Jan 21, 2010 at 11:56 PM, Davis, Sean (NCI) <seandavi at="" gmail.com=""> wrote: > ---------- Forwarded message ---------- > From: Boris Zybailov <boriszybailov at="" gmail.com=""> > Date: Thu, Jan 21, 2010 at 11:51 PM > Subject: Re: [BioC] GEOmetadb query > To: Sean Davis <seandavi at="" gmail.com=""> > > > Thank you for the quick response. > Yes, this is exactly what I need > > On Thu, Jan 21, 2010 at 11:49 PM, Sean Davis <seandavi at="" gmail.com=""> wrote: >> On Thu, Jan 21, 2010 at 11:42 PM, ?<boriszybailov at="" gmail.com=""> wrote: >>> Dear list, >>> >>> I installed GEOmetadb in order to find all the human cancer- related gene >>> expression GEO series, >>> for which there are also aCGH data available. But I can not figure out how >>> to do this and >>> I would really appreciate any advice. >> >> Hi, Boris. ?Just to clarify, you want to find human cancer samples >> with both gene expression and copy number data? > > Hi, Jack. ?I don't think what he wants to do is possible with GEO. > However, I suppose one could pull out all GSEs with both CGH and > expression data and hope those have what he wants (paired human cancer > samples). ?Do you mind following up with one of your masterful > queries? > > Thanks, > Sean >
ADD COMMENTlink written 7.8 years ago by Jack Zhu170
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