Dear team,
I used plugins and created Formulas for dataset analysis and its work only with
each dataset (bioassay) separately; the result is column (Ch1).
Is it possible to make analysis (for example quantile normalization of 3
bioassays, or formula to find mean between bioassay1 (Ch1))and
://baseplugins.thep.lu.se/wiki/net.sf.basedb.normalizers
In general one needs plug-ins to mix information between bioassays so a
BASE Formula will not do.
Hope this helps,
Jari
On 2010-11-25 04.39, Irina 264 wrote:
Dear team,
I used plugins and created Formulas for dataset analysis and its
I am trying to run the RMAExpress plug-in to import Affymetrix data, but I get
the following error:
net.sf.basedb.core.InvalidUseOfNullException: Invalid use of null. The 'design'
value cannot be set to null.
at net.sf.basedb.core.Affymetrix.getCdfFile(Affymetrix.java:126)
Dear team,
I am working with MergeBioAssay plug-in. I created a formula for reporterID
using rep(‘id’) as expression, because other reporter parameters (Name or
ExternalID) don’t work. However, when I run MergeBioAssay with Affy dataset I
have an error message:
“Error: Raw data for raw
2.1
Date: Fri, 20 May 2011 09:21:12 +0200
From: nick...@thep.lu.se
To: basedb-users@lists.sourceforge.net
Subject: Re: [base] reporters on MergeBioAssay plug-in
On 2011-05-20 09:04, Irina 264
Dear Team,
I run Illumina plugin and had error: Java heap space. I have increased
CATALINA OPTS=-Xmx2048m, however now I have the garbage collector problem:
Error: GC overhead limit exceeded
View job -- Run plugin: Illumina raw data importer
java.lang.OutOfMemoryError: GC overhead
Dear team,
I install Tab2MageExporter plugin into /base/plugins directory and addition
copy Tab2MageExporter.jar and ebi-plugins-utils.jar into /base/www/WEB-INF/lib
directory
I have an error message, when I export Experiment with Tab2Mage exporter:
View job -- Run plugin: Tab2Mage exporter
Dear team,
I am working on ‘Tab2Mage exporter’ plugin. I created Agilent experiment and
Validate it with following message:
java.lang.NullPointerException on page /base2/common/overview/index.jsp
Version
BASE 2.16.0 (build #5472; schema #88)
Web server
Apache Tomcat/6.0.29
Database
and biosources or it may not work.
/Nicklas
On 2011-06-10 08:17, Irina 264 wrote:
Dear team,
I am working on ‘Tab2Mage exporter’ plugin. I created Agilent experiment
and Validate it with following message:
java.lang.NullPointerException on page
/base2/common/overview/index.jsp
Dear team,
The idea to analyse data in MeV is great. I successfully transferred data to
MeV, analyzed it and used ‘save to BASE’ function to create new child bioassays
set. However, new created bioassays are the copy of the original one. I don’t
have possibility to transfer the analysis
Ok, thank you
Date: Mon, 27 Jun 2011 08:08:29 +0200
From: nick...@thep.lu.se
To: basedb-users@lists.sourceforge.net
Subject: Re: [base] Save to BASE function in the MeV gui
On 2011-06-24 05:50, Irina 264 wrote:
Dear team,
The idea to analyse data in MeV is great. I successfully
Dear team,
Could you help,
when I try to configure Tab2MageImporter I have following error:
Unexpected error
java.lang.NullPointerException on page /base2/common/plugin/index.jsp
Version
BASE 2.17.2 (build #5659; schema #90)
Web server
Apache Tomcat/6.0.29
Database Server
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