Emmanuel Courcelle wrote: > Hello > > Trying to use BASE with affymetrix data. > I think we missed something... but don't know what > > We have created: > -An array design called ATH1-121501, from the file ATH1-121501.CDF > -Several raw bioassays fro several .cel files, when I click on the > bioassays > -An experiment connected to these bioassays > > the Affiy plugin (with RAMExpress and Plier plugins) is installed. > > We are trying to create a Root BioAssay. > Experiment/Analyze/New Root bioAssay Set > > 1/ There is a blue link on the window, with the message: "Formula > intensity calculator: Raw data for raw data type 'Affymetrix' is not > stored in the database."
This is nothing to worry about. It is coming from the "Formula intensity calculator" plug-in which doesn't work with Affymetrix data. > 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. > I cannot walk > accross the raw data from the Raw Bioassay screen. Is this normal > behaviour with affy data or is there something wrong ? Yes. There is no raw data except the CEL file. I think you can download/view it from raw bioassay page. > > 3/ Neither RMAExpress not Plier plugins work (the corresponding binaries > start, as seen from a "top" on the server, but they end with a stack > trace, I can send you the trace if needed). Since you don't have any reporters, this is probably related to that. /Nicklas ------------------------------------------------------------------------- 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]
