From pavlidis at imbb.forth.gr Sun Oct 16 11:04:45 2005 From: pavlidis at imbb.forth.gr (pavlidis@imbb.forth.gr) Date: Sun Oct 16 12:01:26 2005 Subject: [Bioperl-microarray] question about bioperl and microarrays Message-ID: <1129475085.43526c0d95ba0@webmail.imbb.forth.gr> Hi, I would like to ask if there is any way using bioperl to retrieve microarray datasets from GEO or Stanford Database. I am a newbie in bioperl and perl so I torture myself for days. Specifically I would like to retrieve all the datasets which have a particular gene in them. Thank you very much Pavlos From sherlock at genome.stanford.edu Mon Oct 17 11:45:56 2005 From: sherlock at genome.stanford.edu (Gavin Sherlock) Date: Mon Oct 17 12:16:25 2005 Subject: [Bioperl-microarray] question about bioperl and microarrays In-Reply-To: <1129475085.43526c0d95ba0@webmail.imbb.forth.gr> References: <1129475085.43526c0d95ba0@webmail.imbb.forth.gr> Message-ID: Hi Pavlos, I don't believe that BioPerl has any facility for retrieving data from SMD, and SMD currently doesn't support querying of datasets to see if there exist data for a particular gene. We have implemented a very basic set of Web Services (documented at http://genome- www5.stanford.edu/help/webServices.shtml), which we will flesh out in the future, but the easiest way to retrieve data currently from SMD is from our ftp site, which has data dumps for all published experiments organized by organism (ftp://smd-ftp.stanford.edu/pub/smd/ organisms/). You would then have to parse the datafiles to determine if they had data for your gene(s) of interest, Cheers, Gavin ________________________________________________________ Gavin Sherlock Dept. of Genetics Center for Clinical Sciences Research 269 Campus Drive, Room 2255b, Stanford, CA 94305-5120 Tel: 650 498 6012 Fax: 650 724 3701 On Oct 16, 2005, at 8:04 AM, pavlidis@imbb.forth.gr wrote: > Hi, > I would like to ask if there is any way using bioperl > to retrieve microarray datasets from GEO or Stanford Database. I am > a newbie > in bioperl and perl so I torture myself for days. > Specifically I would like to retrieve all the datasets which have a > particular > gene in them. Thank you very much > > Pavlos > > _______________________________________________ > bioperl-microarray mailing list > bioperl-microarray@bioperl.org > http://portal.open-bio.org/mailman/listinfo/bioperl-microarray >