[base] (no subject)

[Ross C. <ros...@mi...>]

Hi all

I am trying to analyse some data from an Affymetrix GeneChip Mouse Gene 1.0
ST Array [MoGene-1_0-st-v1] chip using the RMAexpress plugin and the CDF
file downloaded from Affymetrix.  The analysis fails with an exception
(below).

Can you advise me of what the underlying problem might be and of any
potential solution.

Many thanks

Ross Chapman

net.sf.basedb.core.BaseException: Unable to import root bioassay.
at se.lu.thep.affymetrix.RMAExpress.storeResult(RMAExpress.java:218)
at
se.lu.thep.affymetrix.AbstractExternalBinaryPlugin.run(AbstractExternalBinaryPlugin.java:263)
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:745)
Caused by: java.io.FileNotFoundException:
/tmp/tomcat6-tomcat6-tmp/RMAExpress plug-in/3983/rma.txt (No such file or
directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:146)
at java.io.FileInputStream.<init>(FileInputStream.java:101)
at se.lu.thep.affymetrix.RMAExpress.storeResult(RMAExpress.java:167)
... 4 more

-- 
Dr Ross Chapman
Senior Bioinformatician
MIMR-PHI Institute of Medical Research
27-31 Wright Street, Clayton, VIC 3168

(03) 99024766