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