extracting phenotypic data from GEO (i.e. GSE8671)
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Andrew Yee ▴ 350
@andrew-yee-2667
Last seen 7.3 years ago
Hi, I've been working with the GEOquery package. I'm interested in creating a phenotypic data file from GSE8671. I imagine this should be possible after using getGEO(), however, it appears to be taking a substantial amount of time to parse through the soft file. Is there a simpler, quicker method of extracting just the phenotypic information? Thanks, Andrew [[alternative HTML version deleted]]
GEOquery GEOquery • 1.4k views
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@sean-davis-490
Last seen 18 minutes ago
United States
On Thu, Jun 4, 2009 at 5:41 PM, Andrew Yee<yee at="" post.harvard.edu=""> wrote: > Hi, I've been working with the GEOquery package. ?I'm interested in creating > a phenotypic data file from GSE8671. ?I imagine this should be possible > after using getGEO(), however, it appears to be taking a substantial amount > of time to parse through the soft file. ?Is there a simpler, quicker method > of extracting just the phenotypic information? Hi, Andrew. You didn't post your sessionInfo(), but in recent versions of GEOquery, the default is to parse the GSEMatrix files when getting GSEs. This is quite a bit faster (typically taking a few seconds for parsing). Sean
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After some e-mail exchanges with Sean, this is what finally works: gse <- getGEO('GSE8671',GSEMatrix=TRUE) pheno.df <- pData(phenoData(gse[[1]])) Note that in this example, gse is not a GSE object anymore. It is a list of ExpressionSets (in this case one expression set). (Also note that I'm running R 2.9.0 on a Windows machine using GEOquery version 2.8.0). Thanks, Andrew On Thu, Jun 4, 2009 at 5:46 PM, Sean Davis <seandavi@gmail.com> wrote: > On Thu, Jun 4, 2009 at 5:41 PM, Andrew Yee<yee@post.harvard.edu> wrote: > > Hi, I've been working with the GEOquery package. I'm interested in > creating > > a phenotypic data file from GSE8671. I imagine this should be possible > > after using getGEO(), however, it appears to be taking a substantial > amount > > of time to parse through the soft file. Is there a simpler, quicker > method > > of extracting just the phenotypic information? > > Hi, Andrew. You didn't post your sessionInfo(), but in recent > versions of GEOquery, the default is to parse the GSEMatrix files when > getting GSEs. This is quite a bit faster (typically taking a few > seconds for parsing). > > Sean > [[alternative HTML version deleted]]
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Andrew Yee wrote: > After some e-mail exchanges with Sean, this is what finally works: > gse <- getGEO('GSE8671',GSEMatrix=TRUE) > pheno.df <- pData(phenoData(gse[[1]])) Hi Andrew -- you can save a few keystrokes with pData(gse[[1]]) Martin > Note that in this example, gse is not a GSE object anymore. It is a list > of ExpressionSets (in this case one expression set). > > (Also note that I'm running R 2.9.0 on a Windows machine using GEOquery > version 2.8.0). > > Thanks, > Andrew > > On Thu, Jun 4, 2009 at 5:46 PM, Sean Davis <seandavi at="" gmail.com=""> wrote: > >> On Thu, Jun 4, 2009 at 5:41 PM, Andrew Yee<yee at="" post.harvard.edu=""> wrote: >>> Hi, I've been working with the GEOquery package. I'm interested in >> creating >>> a phenotypic data file from GSE8671. I imagine this should be possible >>> after using getGEO(), however, it appears to be taking a substantial >> amount >>> of time to parse through the soft file. Is there a simpler, quicker >> method >>> of extracting just the phenotypic information? >> Hi, Andrew. You didn't post your sessionInfo(), but in recent >> versions of GEOquery, the default is to parse the GSEMatrix files when >> getting GSEs. This is quite a bit faster (typically taking a few >> seconds for parsing). >> >> Sean >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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