Reha Yildirimman wrote: > I have another approach and if that seems ineffective to you please > drop me a line!
We also had that approach to begin with. However we were a bit worried about database performance since the Affymtrix chips contains a lot probes. Since most tools needed the CEL and/or CDF files anyway we decided to not put Affymetrix data into the database. > My approach is to change the affymetrix data type > inside the raw-data-type.xml from a simple file-definition to a > database-definition like the other data-types defined inside the xml. You should not change that. I am not sure what will go wrong, but I think there is code that depends on the default setup. We hope to make this more flexible in the future. > I added properties for the values: MEAN (float), STDV (float), > NPIXELS (float) To be able to import data via a base-plugin from a > CEL file each data line has to have an association to a reporter - > thus I added a column holding the ProbeSet ID for each CEL file. > > My problem is that when I associate a CDF file to an array design - > which I need for reference purpose - it states under Properties: **** > Features: Yes(0) **** This will not work unless you also have the CEL file at the raw bioassay. And if you have the CEL file you can't have the data in the database... I would recommend that you use the Affymetrix setup as it is. If you need a different way of calculating the intensity values this should be done by a plug-in. /Nicklas ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
