Hi, The plier and rmaexpress plug-ins calculates the probeset expression values using information from the cel/cdf files. The plugins are presented on the BASE plugin site http://baseplugins.thep.lu.se/wiki/se.lu.thep.affymetrix How the expression values are calculated is presented elsewhere (please follow links from the plugin website).
The raw data for Affymetrix is stored in the original cel files and is not stored in database tables like GenePix and other data. Affymetrix related expression data is not stored in the database tables until the creation of the first root bioassay set. You do not need to create another affymetrix plugin if you are happy with the algorithms provided by plier and rmaexpress. However, if you need something else then you may need to write your own plugin (or help us improve the current affymetrix plugin). You may want to change the extended-properties.xml, some information on this is available here, http://base.thep.lu.se/chrome/site/doc/admin/extended-properties.html The problem with using CDFs in your array design is most likely related to missing reporters (probesets). Have you imported the reporters associated with the design (CDF)? Please read the information provided in the plugin site and http://base.thep.lu.se/chrome/site/doc/user/getting_started.html (nice example on the workflow in BASE with references to Affymetrix data). And, of course, you can also use the mailing list. Cheers, Jari Reha Yildirimman wrote: > Hello, > > like some other people I am trying to import data from affymetrix CEL > files. > Searching the archive I have read that people use the RMAExpress and PLIER > plugins. As far as I understood the plug-in extracts/calculates the > intensities but > where are those data stored, since the associated raw data type for > affymetrix has > no database table definition? > Furthermore, are those intensities the stated MEAN values inside the CEL > file > and are extracted intensities for each coordinate/probe or only for > probe sets ? > > I have another approach and if that seems ineffective to you please drop > me a line! > 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. > 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 makes the raw data importer fail with: > **** > Item not found: Feature[row=null, column=null, block=null, > metaGridX=null, metaGridY=null] on line 2 > **** > > If I take out the connection to the CDF - thus turning the Feature > property to No - the raw data importer works. > How can I get around the problem without having to add to each line > inside the CEL file fake numbers for the features > row, column, block, ... > > Thanks alot in advance. > > Best, > > Reha > > ------------------------------------------------------------------------- > 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] -- Jari Hakkinen, PhD Complex Systems Division mailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Solvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se ------------------------------------------------------------------------- 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]
