Re: [base] MeV: export bioassay set to TDMS file error
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 -- Live Security Virtual Conference 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 threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
Re: [base] MeV: export bioassay set to TDMS file error
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 R* 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 -- Live Security Virtual Conference 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 threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] MeV: export bioassay set to TDMS file error
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 R* to *Rgn R2* to get it to work with my grp extension genepix files. Thanks in Advance Steven Fan -- Live Security Virtual Conference 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 threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
