Hi Jari
Thank you for your comments.
I am using BASE 2.17.2 which is running on a Linux/Ubuntu server.
I have found that RMAExpress runs perfectly with most Affymetrix files, but
I get this error when analysing data from Affymetrix GeneChip Human Gene
1.0 ST or Affymetrix GeneChip Mouse Gene 1.0 ST arrays, so I believe that
the error must lie with the configuration of the ST arrays within base.
I preloaded the probes as reporters into the database from a cdf file for
each array, and the reporters are visible in the database.
Yet somehow the RMAExpress plugin is failing with these arrays.
I would appreciate any comments or suggestions.
Thanks
Ross
On 5 March 2015 at 00:18, basedb-users-requ...@lists.sourceforge.net
wrote:
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Today's Topics:
1. Re: BASE reporter fields problem (Nicklas Nordborg)
2. BASE 3.4 has been released (Nicklas Nordborg)
3. RMAexpress (Ross Chapman)
4. Re: RMAexpress (Jari H?kkinen)
5. BASE 3.4.1 has been released (Nicklas Nordborg)
6. (no subject) (Ross Chapman)
7. Re: Problem with RMAexpress plugin [Was: (no subject)]
(Jari H?kkinen)
-- Forwarded message --
From: Nicklas Nordborg nicklas.nordb...@med.lu.se
To: BASE ML basedb-users@lists.sourceforge.net
Cc:
Date: Mon, 12 Jan 2015 07:50:46 +0100
Subject: Re: [base] BASE reporter fields problem
On 2015-01-12 07:25, Ross Chapman wrote:
Hi all
I recently moved a BASE2 database to a new server by copying the full
database and all installation files along with plugin files.
When I try to run some custom plugins on the new instance, I receive an
error stating that there is an unknown reporter field being requested in
the new database version. The same plugins still work fine on the
original BASE2 application.
Can you point me to where the reporter fields are set and how I can
correct the annotations in the new instance.
This should be in the extended-properties.xml file that is found in the
WEB-INF/classes directory in your BASE installation. See
http://base.thep.lu.se/chrome/site/latest/html/appendix/
extendedproperties.html for some more information.
/Nicklas
-- Forwarded message --
From: Nicklas Nordborg nicklas.nordb...@med.lu.se
To: BASE ML basedb-users@lists.sourceforge.net, BASE dev
basedb-de...@lists.sourceforge.net,
basedb-annou...@lists.sourceforge.net
Cc:
Date: Wed, 14 Jan 2015 14:41:58 +0100
Subject: [base] BASE 3.4 has been released
Hello all,
After fixing a few issues with the beta version, BASE 3.4.0 has now
been released. One new feature is the possibility to install skins. Check
out the example skins at
http://baseplugins.thep.lu.se/wiki/net.sf.basedb.skincollection
For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.4group=type
Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html
As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage
/Nicklas
-- Forwarded message --
From: Ross Chapman ross.chap...@mimr-phi.org
To: basedb-users@lists.sourceforge.net
Cc:
Date: Tue, 3 Feb 2015 16:55:30 +1100
Subject: [base] RMAexpress
Hi all
I am having problems running the RMAexpress plug in after migrating BASE2
to a new server.
The plug in fails with the following error:
java.io.IOException: Unexpected exit of RMAExpress sub-process. Return
value: 127
at se.lu.thep.affymetrix.RMAExpress.runBinary(RMAExpress.java:156)
at
se.lu.thep.affymetrix.AbstractExternalBinaryPlugin.run(AbstractExternalBinaryPlugin.java:262)
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)
Can you suggest a possible cause and solution?
Many thanks
Ross
--
Dr Ross Chapman
Senior Bioinformatician
MIMR-PHI Institute of Medical Research
27-31 Wright Street, Clayton, VIC 3168
(03) 99024766
-- Forwarded message --
From: Jari Häkkinen jari.hakki...@med.lu.se
To: basedb-users@lists.sourceforge.net
Cc:
Date: Tue, 03 Feb 2015 14:20:45 +0100
Subject: Re: [base] RMAexpress
Hi,
Did you also move the underlying RMAexpress binary to the new server? You
probably need to recompile RMAExpress (http://rmaexpress.bmbolstad.com/)
for your new server.
Jari
On
