converting GEO soft files to MS excel files
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@dr-gyorffy-balazs-619
Last seen 7.1 years ago
Hi All! How can I convert data files downloadable from the GEO depository to EXCEL files? The GEO files have the SOFT extension, and they contain all data in one text file, which I want to convert to a table. Thanks in advance Balazs ------------------------- Bal?zs GY?RFFY MD, PhD Semmelweis University Budapest Szent?gothai J?nos Knowledge Centre, B?kay u. 53/54, Budapest, H-1088 Hungary Tel: +36 1 266 0926 /2725 Fax: +36 1 303 6077 Email: zsalab2 at yahoo.com
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@sean-davis-490
Last seen 6 weeks ago
United States
On Wednesday 06 December 2006 10:35, Dr_Gyorffy_Balazs wrote: > Hi All! > > How can I convert data files downloadable from the GEO depository to EXCEL > files? The GEO files have the SOFT extension, and they contain all data in > one text file, which I want to convert to a table. You can use the GEOquery package to do this. GEOquery will help you to parse and manipulate the SOFT format file into Bioconductor objects, which you can then output in whatever format you see fit. Sean
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@sean-davis-490
Last seen 6 weeks ago
United States
On Wednesday 06 December 2006 11:19, Dr_Gyorffy_Balazs wrote: > Thank you for your prompt answer. However, when I try to use getGeo, the > URL used is not correct. > > getGeo tries following url> > ftp://ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE3149/GSE3149_fa mily.so >ft.gz You will need to update your GEOquery to version 1.9.0 which should fix the process. Sean
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@sean-davis-490
Last seen 6 weeks ago
United States
On Friday 15 December 2006 06:15, Dr_Gyorffy_Balazs wrote: > Dear Sean, > > GEOquery is OK, but I have an additional question: is it possible to load > the downloaded .tz file in order no to stay online all the parsing time? The parsing is not done "online". The .tar.gz file is first downloaded to a temporary directory (the location of which is printed to the screen after the download for later use). If you already have a .tar.gz file downloaded, you can supply the filename to the getGEO() function to skip the download part. See the help for getGEO(). Hope that helps. Sean
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