Steve Taylor wrote:
I think you have mailed or filed a bug reporter about a similar problem
before. See ticket #520: http://base.thep.lu.se/ticket/520
The problem was fixed in 2.2.3 so you need to upgrade your BASE
installation to something newer.
/Nicklas
> Hi,
>
> I have extended BASE2.2.1 (MySQL Distrib 5.0.27) to accept ScanArray
> files (very similar to GenePix) by changing extended-properties.xml
> and updating the database.
>
> The extended-properties.xml the intensity formula I am using is:
>
> <intensity-formula name="normalised_ratio_of_means" title="Ch1
> Normalised Mean / Ch2 Normalised Mean" description="Ch1 Normalised
> Mean / Ch2 Normalised Mean" > <formula channel="1"
> expression="raw('ch1NMean')" /> <formula channel="2"
> expression="raw('ch2NMean')" /> </intensity-formula>
>
> I have uploaded some data in 'raw bioassay', but when I try and
> create a 'New root bioassay set' I get what looks like a MySQL error.
>
>
> Error: Run plugin: Formula intensity calculator Data truncation: Out
> of range value adjusted for column 'ch1' at row 1
>
> The stack trace is:
>
> net.sf.basedb.core.BaseException: Data truncation: Out of range value
> adjusted for column 'ch1' at row 1 at
> net.sf.basedb.core.SpotBatcher.flush(SpotBatcher.java:161) at
> net.sf.basedb.core.AbstractBatcher.close(AbstractBatcher.java:117) at
> net.sf.basedb.util.IntensityCalculatorUtil.createRootBioAssaySet(IntensityCalculatorUtil.java:447)
> at
> net.sf.basedb.plugins.IntensityCalculatorPlugin.run(IntensityCalculatorPlugin.java:256)
> at
> net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:88)
> at
> net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:420)
> at java.lang.Thread.run(Thread.java:595) Caused by:
> java.sql.BatchUpdateException: Data truncation: Out of range value
> adjusted for column 'ch1' at row 1 at
> com.mysql.jdbc.ServerPreparedStatement.executeBatch(ServerPreparedStatement.java:665)
> at
> com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeBatch(NewProxyPreparedStatement.java:1723)
> at net.sf.basedb.core.SpotBatcher.flush(SpotBatcher.java:155) ... 6
> more
>
> Can someone explain what this message means and what the Formula
> Intensity Calculator is trying to do here?
>
> Thanks for any help,
>
> Steve
>
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