Thanks Nicklas, I'll go through the links you provided. Marco.
> > Re: [base] Importing Annotations for Affymetrix Array designs > > Nicklas Nordborg > Tue, 12 May 2009 10:42:48 -0700 > > Zak Mc Kracken wrote: >> Hi all, >> >> Does anyone know the details about importing probeset annotations for >> Affymetrix chips? >> >> I was able to import a couple of CDFs provided by the Affy web site, >> then I tried the "CSV importer x" (from LIMS->Array Designs menu), >> providing the CSV annotation file as input, which, again, I downloaded >> from Affy-web. > > I don't know anything about the "CSV importer x". If it appears in the > Array designs menu it is probably used to import array designs, not > reporter annotations. Reporter annotations are imported from the View -> > Reporters menu. By the way, Affymetrix array designs doesn't import > their probesets the database. For performance reasons, they are kept in > the CDF file. > >> However, it doesn't seem that the probeset IDs are complemented with the >> further information coming from the CSV. In fact, in the reporter >> section of the BASE UI, I cannot find essential columns such as GO >> accessions and labels, or KEGG IDs. > > It is possible to customize the reporter annotation. The documentation > describes how to do it: > http://base.thep.lu.se/chrome/site/latest/html/appendix/appendix.extendedproperties.html > > >> How does the thing work? How does it work in general (I started with >> Affy, but later I will need to work with Illumina chips as well)? >> >> Moreover, I am trying to do that in order to use BASE as a single point >> storage for both visualizing the probeset annotations and accessing them >> from external Java programs. Can someone point me to the right API parts >> and documentation for doing that? >> > > API documentation is available at > http://base.thep.lu.se/chrome/site/latest/api/index.html and a lot of > user and developer documentation at > http://base.thep.lu.se/chrome/site/latest/html/index.html > > /Nicklas > ------------------------------------------------------------------------------ Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
