Re: [base] basedb-users Digest, Vol 70, Issue 1

2015-03-10 Thread Ross Chapman
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
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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

[base] (no subject)

2015-03-03 Thread Ross Chapman
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
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[base] RMAexpress

2015-02-02 Thread Ross Chapman
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
--
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/___
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject unsubscribe to
basedb-users-requ...@lists.sourceforge.net


[base] BASE reporter fields problem

2015-01-11 Thread Ross Chapman
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.

Many thanks

Ross

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

(03) 99024766
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[base] reseting root password

2014-02-16 Thread Ross Chapman
Hi all

I have inherited the management of a BASE 2 solution for managing
microarray data.

I do not have access to the Root password, but I do have administrator
rights.

Am I able to reset the root password, will this have any impact on how BASE
operates?

Thanks for your help.

Regards

Ross
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[base] Agilent and LIMMA in BASE

2012-04-27 Thread Ross Chapman
Hi

I want to analyse Agilent microarrays in BASE 2.17.2 using LIMMA methods to
perform background subtraction, normalisation and significance testing.

Does anyone know if there is a suitable plugin available to perform these
analyses?

Thanks

Ross
-- 
Dr Ross Chapman
Senior Bioinformatician
MIMR

(03) 99024719
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