from "Stack trace" tab:
View job -- Run plugin: Base1PluginExecuter
Name
Run plugin: Base1PluginExecuter
Description
Priority
5 (1 = highest, 10 = lowest)
Status
Error:
Raw data for raw data type: Affymetrix
is not stored in the database.
Percent complete
unknown
100%
Created
2011-05-20 18:10:30
Scheduled
2011-05-20 18:11:10
Started
2011-05-20 18:11:28
Ended
2011-05-20 18:11:42
Running time
14 seconds
Server
vera097.its.monash.edu.au
Job agent
- none -
User
Irina Rusinova
Experiment
E-GEOD-6257
Plugin
Base1PluginExecuter
(version 2.16.0)
Configuration
MergeBioAssay
net.sf.basedb.core.BaseException: Raw
data for raw data type: Affymetrix is not stored in the database.
at
net.sf.basedb.core.DynamicSpotQuery.joinRawData(DynamicSpotQuery.java:261)
at
net.sf.basedb.util.importer.spotdata.BaseFileImporter.createChildRawDataMapping(BaseFileImporter.java:510)
at
net.sf.basedb.util.importer.spotdata.BaseFileImporter.doImport(BaseFileImporter.java:346)
at
net.sf.basedb.plugins.Base1PluginExecuter.importData(Base1PluginExecuter.java:1471)
at
net.sf.basedb.plugins.Base1PluginExecuter.run(Base1PluginExecuter.java:774)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:116)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:510)
at java.lang.Thread.run(Thread.java:636)
> Date: Fri, 20 May 2011 09:21:12 +0200
> From: nick...@thep.lu.se
> To: basedb-users@lists.sourceforge.net
> Subject: Re: [base] reporters on MergeBioAssay plug-in
>
> On 2011-05-20 09:04, Irina 264 wrote:
> > Hi Nicklas,
> >
> > Thanks for the quick reply.
> >
> > I run RMAExpress with Affy data, then I done filtering with equal size
> > of arrays afterwards.
> >
> > Then I run MergeBioAssay (with Base1pluginExecuter) to find average
> > between replicates (grouping assays by control and treatment with method
> > ‘arithmetic mean of intensity) and have this error message: “Error: Raw
> > data for raw data type: Affymetrix is not stored in the database.”
> >
> > When I use Agilent data, i have no problems.
> >
> > Did I explain better?
>
> Yes... but I still have no idea why the error about raw data is coming
> up... As far as I know the Merge BioAssay plug-in doesn't use raw data
> for the calculations. It would be useful to get a complete stacktrace of
> the error in order to locate the source of the problem.
>
> Do you get the error while you are configuring the job? If so you should
> be able to display more error information by clicking on the little [+]
> icon in the configuration wizard.
>
> Or, if you get the error while the plug-in is running, there is a "Stack
> trace" tab in the job dialog.
>
>
> /Nicklas
>
>
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