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 ------------------------------------------------------------------------------ The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com _______________________________________________ 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
