Re: [base] basedb-users Digest, Vol 70, Issue 1
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, wrote: > Send basedb-users mailing list submissions to > basedb-users@lists.sourceforge.net > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/basedb-users > or, via email, send a message with subject or body 'help' to > basedb-users-requ...@lists.sourceforge.net > > You can reach the person managing the list at > basedb-users-ow...@lists.sourceforge.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of basedb-users digest..." > > 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 > To: BASE ML > 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 > To: BASE ML , 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+3.4&group=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 > 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$JobRunner.run(InternalJobQueue.java:510) > at java.lang.Thread.run(Thread.java:745) > > Can you suggest a possible cause and solution? > > Many thanks > > Ross > > -- > Dr Ross Chapman > Senior Bioinformatician > MIMR-PHI Institute of Medical Research > 27-31 Wright Street, Clayton, VIC
[base] (no subject)
Hi all I am trying to analyse some data from an Affymetrix GeneChip Mouse Gene 1.0 ST Array [MoGene-1_0-st-v1] chip using the RMAexpress plugin and the CDF file downloaded from Affymetrix. The analysis fails with an exception (below). Can you advise me of what the underlying problem might be and of any potential solution. Many thanks Ross Chapman net.sf.basedb.core.BaseException: Unable to import root bioassay. at se.lu.thep.affymetrix.RMAExpress.storeResult(RMAExpress.java:218) at se.lu.thep.affymetrix.AbstractExternalBinaryPlugin.run(AbstractExternalBinaryPlugin.java:263) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:116) at net.sf.basedb.core.InternalJobQueue$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.(FileInputStream.java:146) at java.io.FileInputStream.(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 -- 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] 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 -- 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
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 -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. vanity: www.gigenet.com___ 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] reseting root password
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 -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk___ 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] Agilent and LIMMA in BASE
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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ 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
