On Mon, Dec 02, 2002 at 03:34:02PM +0100, AlessandroSemeria at cramont.it wrote:> Hello! I don't know if there is some R-package able > to associate ontology to a long list of UniGene Name (a txt-tab file or > an XML file), or > if the best way is a Perl script. > Some suggestion? Thanks!It depends on where the UniGene names come from and whether we have already done a mapping (for example if they were from some commonly used Affymetrix chips then it would be relatively easy). If not, you need to do the mapping - what is easiest depends on what you know, for me R is usually easier than Perl for many others it goes the other way...but really, you need to be a bit more specific about what you are trying to do if you want anyone to help you.> > A. S. > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > stat.math.ethz.ch/mailman/listinfo/r-help-- +---------------------------------------------------------------------------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | Harvard School of Public Health email: rgentlem at jimmy.dfci.harvard.edu | +---------------------------------------------------------------------------+
My file come from features extraction sw Agilent and I forgot to say in previous message that I have the sistematic name too (i.e. gene name recognized from GenBank), what you means with "mapping"? Thanks! Best! A. S. ---------------------------- Sincerely yours. |------------------------------------+------------------------------------| |Alessandro Semeria |Tel. +39 544 536811 | |------------------------------------+------------------------------------| |Models and Simulation Laboratory |Fax. +39 544 538663 | |------------------------------------+------------------------------------| |The Environment Research Center - | | |Montecatini (Edison Group), Via | | |Ciro Menotti 48, |E-mail: asemeria at cramont.it | |48023 Marina di Ravenna (RA), Italy | | |------------------------------------+------------------------------------|
Hello! I don't know if there is some R-package able to associate ontology to a long list of GeneBank Name (a txt-tab file or an XML file), i.e. I would as output a formatted file with 4 columns (1:GeneBank Name 2,3,4:ontology). I know that I have to perform a mapping of genes, I got a look on AnnBuilder pkg, but I 've not idea from where to start. Some suggestion? Thanks in advance! A. S.