Hello, Just a couple of things regarding using Affymetrix with BASE.
i. We are just about to release a plugin to create ArrayDesigns from a bunch of zipped CDF files. This should speed up part of the process of managing Affymetrix Designs. Will post when ready. ii. I have a little simple perl script that connects to Affymetrix web site and retrieves the annotations files, converts those from csv to tab delimited so they are ready to be used for importing Reporters in conjonction with the Affymetrix Reporter Importer Plugin configuration. I have had pb using the csv file from Affymetrix as there are 'comma' used as separator within a field. Depending on how much one wants to store of the Affymetrix annotations, the extended-properties.xml file may have to be modified, and the database upgraded before running the plugin. If not, then those files can used to load ProbeSet ID (email me offline for the script). For the moment, sorry folks, no plugin for batch importing the reporters from a bunch of annotation files.... iii. For information only, I have managed to configure and run RMAExpress and PLIER plugin on windows machine. Have to add to the documentation. cheers Philippe Bob MacCallum wrote: > > Emmanuel Courcelle wrote: > > > Hello > > > > > > Trying to use BASE with affymetrix data. > > me too! > > > > 2/ I can't see any new Reporter in the View/Reporters > > > > You need to import the reporter from a reporter annotation file (.csv). > > See > > > http://lev.thep.lu.se/trac/baseplugins/browser/tags/se/lu/thep/affymetrix-0.6/README > > for details. > > could someone point me to these .csv files please? > > I've downloaded the xxx_libraryfile.zip (containing a .cdf file amongst > others) but no .csv file. Do you get this from NetAffx online? > > many thanks, > Bob. > > -- **************************************************************** Philippe Rocca-Serra (Ph.D) NET Project - Technical Coordinator http://www.ebi.ac.uk/net-project EBI- The European Bioinformatics Institute EMBL Outstation Hinxton Wellcome Trust Genome Campus CB10 1SD Cambridge, UK email: [EMAIL PROTECTED] Tel: +44 (0) 1223 492 553 Fax: +44 (0) 1223 494 468 European Nutrigenomics Organization http://www.nugo.org **************************************************************** ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
