Re: [base] MeV: export bioassay set to TDMS file error

2012-06-14 Thread Nicklas Nordborg
On 2012-06-07 08:52, Nicklas Nordborg wrote:
 On 2012-06-05 22:52, Steven Charles Fan wrote:
 Running base v3.1.1 with mev-launcher-1.9 binary (current base version
 and MeV version 4.7.3) on Centos6. Tried to export a bioassay set of two
 bioassays to a TDMS file for analysis in MeV and got a unnamed error
 with the following stack trace:
 ...
 Is this a user error I can do something about or have I stumbled upon
 a bug?

 I can confirm that this is indeed a bug. Until a fix has been released,
 the workaround is to use the 'Clone reporters' function on the
 experiment view page.

I have now release a new version of the MeV plug-in (1.10). It fixes 
this bug and also update MeV to 4.8.1. It can be downloaded from:

http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev

/Nicklas

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Re: [base] MeV: export bioassay set to TDMS file error

2012-06-07 Thread Nicklas Nordborg
On 2012-06-05 22:52, Steven Charles Fan wrote:
 Running base v3.1.1 with mev-launcher-1.9 binary (current base version
 and MeV version 4.7.3) on Centos6. Tried to export a bioassay set of two
 bioassays to a TDMS file for analysis in MeV and got a unnamed error
 with the following stack trace:
...
  Is this a user error I can do something about or have I stumbled upon 
a bug?

I can confirm that this is indeed a bug. Until a fix has been released, 
the workaround is to use the 'Clone reporters' function on the 
experiment view page.

 The following is unrelated, but I was wondering if reporters were best
 imported from a gpr file or GAL file or if there is a difference. I was
 also wondering if there was a way to update biological annotations
 automatically from SGD.

It shouldn't really matter since the only reporter information in gpr 
and gal files are the reporter id. Annotations need to come from a 
different source. I do not know what SGD is, but in any case there is no 
function to update annotations automatically from any external source. 
It must be done manually by exporting and importing files.

 Oh and a (possible) bug notice: in the *Genepix raw data cy5/cy3
 (cy5/cy3) import configuration* for the *raw bioassay import from file*,
 I had to change *Rgn Rsuperscipt 2* to *Rgn R2* to get it to work with
 my grp extension genepix files.

It's not really a bug. The data files we have all have R² (superscript). 
My guess is that it depends on the Genepix software version and/or 
settings in the software.

/Nicklas

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[base] MeV: export bioassay set to TDMS file error

2012-06-05 Thread Steven Charles Fan
Running base v3.1.1 with mev-launcher-1.9 binary (current base version and
MeV version 4.7.3) on Centos6. Tried to export a bioassay set of two
bioassays to a TDMS file for analysis in MeV and got a unnamed error with
the following stack trace:

java.lang.NullPointerException
  at
net.sf.basedb.mev.export.TdmsExporter.addReporterFields(TdmsExporter.java:290)
  at
net.sf.basedb.mev.export.TdmsExporter.beginExport(TdmsExporter.java:107)
  at
net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter.doExport(AbstractBioAssaySetExporter.java:277)
  at
net.sf.basedb.mev.plugin.TdmsExporterPlugin.performExport(TdmsExporterPlugin.java:263)
  at
net.sf.basedb.core.plugin.AbstractExporterPlugin.run(AbstractExporterPlugin.java:144)
  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:662)

Is this a user error I can do something about or have I stumbled upon a bug?

The following is unrelated, but I was wondering if reporters were best
imported from a gpr file or GAL file or if there is a difference. I was
also wondering if there was a way to update biological annotations
automatically from SGD.

Oh and a (possible) bug notice: in the *Genepix raw data cy5/cy3 (cy5/cy3)
import configuration* for the *raw bioassay import from file*, I had to
change *Rgn Rsuperscipt 2* to *Rgn R2* to get it to work with my grp
extension genepix files.

Thanks in Advance
Steven Fan
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Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
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