Hi Nicklas,
> 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
Ah, yes it's the same problem...thanks for fixing it.
>
> The problem was fixed in 2.2.3 so you need to upgrade your BASE
> installation to something newer.
>
Ok. Thanks for the advice. As stated in the bug report if you have an array
design this also prevents the problem from occurring.
Steve
> /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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