Thanks, I look forwatd to this.
irina
> Date: Fri, 20 May 2011 11:01:39 +0200
> From: nick...@thep.lu.se
> To: basedb-users@lists.sourceforge.net
> Subject: Re: [base] reporters on MergeBioAssay plug-in
>
> Thanks for the stacktrace. It seems to be a bug in the
> Base1PluginExecuter plug-in. It is trying to remap the raw data
> associations after the bioassays have been merged. Obviously, this is
> not possible if there is no raw data stored in the first place. The
> Base1PluginExecuter need to be fixed with a check for this case.
>
> I have created a ticket for this fix to be included with the BASE 2.17.2
> release. Unfortunately there is no workaround.
>
> http://base.thep.lu.se/ticket/1610
>
> /Nicklas
>
>
>
> On 2011-05-20 10:12, Irina 264 wrote:
> >
> >
> > from "Stack trace" tab:
> >
> >
> >
> > View job -- Run plugin: Base1PluginExecuter
> >
> > <javascript:Main.openTabControlHelp('7a1ebdaa616cc46f',%20'main',%20'null')>
> >
> > 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
> > >
> > >
> > >
> > ------------------------------------------------------------------------------
> > > What Every C/C++ and Fortran developer Should Know!
> > > Read this article and learn how Intel has extended the reach of its
> > > next-generation tools to help Windows* and Linux* C/C++ and Fortran
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> > > http://p.sf.net/sfu/intel-dev2devmay
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> >
> >
> >
> > ------------------------------------------------------------------------------
> > What Every C/C++ and Fortran developer Should Know!
> > Read this article and learn how Intel has extended the reach of its
> > next-generation tools to help Windows* and Linux* C/C++ and Fortran
> > developers boost performance applications - including clusters.
> > http://p.sf.net/sfu/intel-dev2devmay
> >
> >
> >
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>
> ------------------------------------------------------------------------------
> What Every C/C++ and Fortran developer Should Know!
> Read this article and learn how Intel has extended the reach of its
> next-generation tools to help Windows* and Linux* C/C++ and Fortran
> developers boost performance applications - including clusters.
> http://p.sf.net/sfu/intel-dev2devmay
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------------------------------------------------------------------------------
What Every C/C++ and Fortran developer Should Know!
Read this article and learn how Intel has extended the reach of its
next-generation tools to help Windows* and Linux* C/C++ and Fortran
developers boost performance applications - including clusters.
http://p.sf.net/sfu/intel-dev2devmay
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