GEOQuery - from a LOCAL SOFT file to an ExprSet object

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michael watson IAH-C ★ 3.4k

@michael-watson-iah-c-378

Last seen 10.3 years ago

Dear All Having read the GEOQuery documentation, there are commands which fetch SERIES files from the web and convert to ExprSet, and there are commands that take a GDS and convert to ExprSet - however, for some reason, my R connection to NCBI works only in about 20% of cases - connections to all other websites are fine - and I simply want to get the file myself (SOFT or SERIES, I don't mind), store it locally and open it in getGEO and convert to an ExprSet object. Is that possible? Mick Head of Informatics Institute for Animal Health Compton Berks RG20 7NN 01635 578411 http://www.iah.ac.uk/research/bioinformatics/bioinf.shtml The information contained in this message may be confide...{{dropped:14}}

convert GEOquery convert GEOquery • 1.3k views

ADD COMMENT • link updated 16.3 years ago by Sean Davis 21k • written 16.3 years ago by michael watson IAH-C ★ 3.4k

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Sean Davis 21k

@sean-davis-490

Last seen 4 months ago

United States

On Tue, Sep 16, 2008 at 8:33 AM, michael watson (IAH-C) <michael.watson at="" bbsrc.ac.uk=""> wrote: > Dear All > > Having read the GEOQuery documentation, there are commands which fetch > SERIES files from the web and convert to ExprSet, and there are commands > that take a GDS and convert to ExprSet - however, for some reason, my R > connection to NCBI works only in about 20% of cases - connections to all > other websites are fine - and I simply want to get the file myself (SOFT > or SERIES, I don't mind), store it locally and open it in getGEO and > convert to an ExprSet object. > > Is that possible? With everything except GSEMatrix, it is possible. See the filename argument in getGEO. I am adding GSEMatrix file parsing in the near future. Sean

ADD COMMENT • link 16.3 years ago Sean Davis 21k

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Sean Davis wrote: > On Tue, Sep 16, 2008 at 8:33 AM, michael watson (IAH-C) > <michael.watson at="" bbsrc.ac.uk=""> wrote: >> Dear All >> >> Having read the GEOQuery documentation, there are commands which fetch >> SERIES files from the web and convert to ExprSet, and there are commands >> that take a GDS and convert to ExprSet - however, for some reason, my R >> connection to NCBI works only in about 20% of cases - connections to all >> other websites are fine - and I simply want to get the file myself (SOFT >> or SERIES, I don't mind), store it locally and open it in getGEO and >> convert to an ExprSet object. >> >> Is that possible? > > With everything except GSEMatrix, it is possible. See the filename > argument in getGEO. I am adding GSEMatrix file parsing in the near With the proviso that it is ExpressionSet's that are wanted. ExprSet's are deprecated. > future. > > Sean > > _______________________________________________ > 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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

ADD REPLY • link 16.3 years ago rgentleman ★ 5.5k

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On Tue, Sep 16, 2008 at 12:35 PM, Robert Gentleman <rgentlem at="" fhcrc.org=""> wrote: > > > Sean Davis wrote: >> >> On Tue, Sep 16, 2008 at 8:33 AM, michael watson (IAH-C) >> <michael.watson at="" bbsrc.ac.uk=""> wrote: >>> >>> Dear All >>> >>> Having read the GEOQuery documentation, there are commands which fetch >>> SERIES files from the web and convert to ExprSet, and there are commands >>> that take a GDS and convert to ExprSet - however, for some reason, my R >>> connection to NCBI works only in about 20% of cases - connections to all >>> other websites are fine - and I simply want to get the file myself (SOFT >>> or SERIES, I don't mind), store it locally and open it in getGEO and >>> convert to an ExprSet object. >>> >>> Is that possible? >> >> With everything except GSEMatrix, it is possible. See the filename >> argument in getGEO. I am adding GSEMatrix file parsing in the near > > With the proviso that it is ExpressionSet's that are wanted. ExprSet's are > deprecated. Good point, Robert. I have added GSEMatrix file parsing to the devel version of GEOquery. It should be available in a day or so after the build system gets through with it. Sean

ADD REPLY • link 16.3 years ago Sean Davis 21k

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