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Hi, I haven't any hands-on experience on this, and maybe/hopefully other ppl will respond as well, but apparently "Celcius" is able to handle such task. http://genome.ucla.edu/wiki/index.php/Celsius copy/paste from their website: http://genome.ucla.edu/wiki/index.php/Celsius_cookbook#.23_Retrieve_sa mple_data_based_on_a_GEO_GSE_identifier # Retrieve sample data based on a GEO GSE identifier # We can retrieve data based on identifiers from other databases as well, such as Array Express and GEO. The identifiers may refer to single samples, or to groups of samples. Here we retrieve the GEO GSE6210 identifier. It refers to a group of 12 HG-U133A samples. GSE6210 = makeExprSet(celsius,id = c("GSE6210"), mapids = TRUE) HTH, Guido ________________________________ From: bioconductor-bounces@stat.math.ethz.ch on behalf of Tim Smith Sent: Thu 13/03/08 22:31 To: bioc Subject: [BioC] getGEO - getting the .CEL files from GEO Hi, Is there any way that I can get the raw .CEL files using getGEO in R? I don't want to use the SOFT files, since I don't know what kind of normalization has been done on them. thanks! PS: I have also checked the previous emails on this topic, and still can't make out what I need to do to get the files. __________________________________________________ [[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

On Thu, Mar 13, 2008 at 5:31 PM, Tim Smith <tim_smith_666 at="" yahoo.com=""> wrote: > Hi, > > Is there any way that I can get the raw .CEL files using getGEO in R? I don't want to use the SOFT files, since I don't know what kind of normalization has been done on them. > > thanks! > > PS: I have also checked the previous emails on this topic, and still can't make out what I need to do to get the files. Hi, Tim. I haven't added a helper to do this because the supplemental files at GEO can contain ANYTHING. However, if you know that you have a set of samples that contain supplemental .cel files, the process is trivial. This page http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_paccess.html#FTP shows you exactly where the files are. You can use download.file() to loop through the GSM # or just download 1 large file via GSE number. I suggest using getGEO() to get the soft format that includes the metadata and platform information. Then, simply replace the exprs() with the locally-processed data. You might think that GEOquery could do all of this for you, and for affy, it could, but for the 4000 other microarray platforms in GEO, it really isn't possible to do so. Hope that helps. Sean