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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