[base] affymetrix

responding binaries start, as seen from a "top" on the server, but they end with a stack trace, I can send you the trace if needed). Thanks in advance, -- Emmanuel COURCELLE[EMAIL PROTECTED] L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50 B.P.52627

[base] Base and webservices

Hello Just to have some information about the future: Are there any plans to use some or all functionalities of BASE through some web service ? Do you have some documentation about this, is there anything already running (even experimental) ? Thanks in advance -- Emmanuel COURCELLE

[base] update 2.1 => 2.2.0: fixed

as. I did what you suggested, I executed ./updateindexes.sh, everything is OK now Great ! -- Emmanuel COURCELLE[EMAIL PROTECTED] L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50 B.P.52627 - 31326 CASTANET TOLO

[base] couldn't update to 2.2.0

org.hibernate.loader.Loader.getResultSet(Loader.java:1778) at org.hibernate.loader.Loader.doQuery(Loader.java:662) at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:224) at org.hibernate.loader.Loader.doList(Loader.java:2

Re: [base] Imagene data format

Nicklas Nordborg a écrit : > Emmanuel Courcelle wrote: > >> Hello >> >> I am trying to configuration the Raw data importer plugin for use with >> Imagene files. >> I do not know how to map theproperties Block, MetaGridX, MetaGridY >> >> 1/ The

[base] Imagene data format

dX", "MetaGridY" in the file, but there are a "Meta Row" and "Meta Column" fields: may I just assign the Imagene's Meta Row to MetaGridX, and the Imagene's Meta Column to MetaGridY ? Thanks in advance, -- Emmanuel COURCELLE[EMAIL PROT

[base] null reporter

nnot be set to null. on line 1178: null" Is there a solution other than skipping or renaming this gene ? -- Emmanuel COURCELLE[EMAIL PROTECTED] L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50

[base] pb with spot images

checked the .zip produced file, I discovered a lot of black image files. So nothing was calculated: is there anything special to install to get this functionality to work ? -- Emmanuel COURCELLE[EMAIL PROTECTED] L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50 B.P.52627

[base] Delay before starting plugin

Hello When I click to start a plugin, the system waits a certain amount of time (tipycally 1 mn). Why is there such a delay ? Is it possible to shorten it ? Please note the machine is not particularly loaded, I am alone (for now) working with Base. -- Emmanuel COURCELLE[EMAIL

Re: [base] Réplicates in base 2

and 0 Reporters ? -Why an extra value called JE_nbrOfElements is created as a last stuff ? -- Emmanuel COURCELLE[EMAIL PROTECTED] L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50 B.P.52627 - 31326 CASTAN

Re: [base] Réplicates in base 2

Nicklas Nordborg a écrit : Emmanuel Courcelle wrote: Hello We are trying to create an experiment composed with: -4 slides -3 times each reporter on each slide So, we have up to 12 replicates for each reporter (sometimes less because some flagged spots were filtered out). How

[base] Réplicates in base 2

than 77000 ? Thanks -- Emmanuel COURCELLE[EMAIL PROTECTED] L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50 B.P.52627 - 31326 CASTANET TOLOSAN Cedex - FRANCE -- - Take Surveys. Earn Cash

Re: [base] JEP extra value calculator again...

set to. > Right, Micha, some files and directories did in fact belong to root The pb is fixed now Thanks for your help ! -- Emmanuel COURCELLE[EMAIL PROTECTED] L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50 B.P.52627 - 31326

[base] JEP extra value calculator again...

rocessConnection(Http11BaseProtocol.java:664) ...at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527) ...at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80) ...at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684) ...at ja

Re: [base] Offline files

What does mean to "move offline" ? Is it the same as: Delete THEN Empty trash ? -- Emmanuel COURCELLE[EMAIL PROTECTED] L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50 B.P.52627 - 31326 CASTANET TOLOSAN Cede

Re: [base] pb with jsvc/Tomcat: fixed

;s better when you know the trick... -- Emmanuel COURCELLE[EMAIL PROTECTED] L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50 B.P.52627 - 31326 CASTANET TOLOSAN Cedex - FRANCE -- - Take Surveys. Earn

[base] pb with jsvc/Tomcat

ashes with the message: "X11 connection rejected because of wrong authentication." Any idea ? -- Emmanuel COURCELLE[EMAIL PROTECTED] L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50 B.P.52627 - 31326 CASTANET TOLOSAN

[base] JEP extra value calculator

have to create a new extra value type: he then asks me for an External ID. What does this mean ? I did not find anything about this in the documentation. -- Emmanuel COURCELLE[EMAIL PROTECTED] L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50 B.P.52627 - 31326 CASTANET TO

[base] how to import reporters ?

ried the Reporters screen, but I found only buttons labelled New Delete New reporterl list Export, there is no import button... -- Emmanuel COURCELLE[EMAIL PROTECTED] L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-5

[base] Plugin configuration (still some pb)

\X\ Y \Y\ -- Emmanuel COURCELLE[EMAIL PROTECTED] L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50 B.P.52627 - 31326 CASTANET TOLOSAN Cedex - FRANCE -- - Using T

Re: [base] Plugin configuration (nearly fixed !)

> > The only significant change you have made is Rgn R? to Rgn R. Does it > still work if you change this to "Rgn R\E.\Q"? > > Great: I took the autogenerated regex, replaced Rgn ? by Rgn R\E.\Q without changing anything else and it worked. However, I changed also the columns parameters, act

[base] Cannot import raw data file to a Raw bioassays

of ratios\Ratios SD\ Rgn R2 \Rgn R.\ Rgn ratio \Rgn Ratio\ Raw data type genepix Reporter ID \ID\ Row \Row\ Remove quotes true X \X\ Y \Y\ -- Emmanuel COURCELLE[EMAIL PROTECTED] L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-

[base] Plugin configuration (nearly fixed !)

Nicklas Nordborg a écrit : > Emmanuel Courcelle wrote: > >> Hi Nicklas >> >> Here are the first 44 lines of the file >> I tried to dos2unix-ify, it did not change anything for Base. >> >> Thanks for your help ! >> > > > I have now te

[base] 2 questions about Plugin configuration

ration ? Or is this the field Header regexp ? Regards, -- Emmanuel COURCELLE[EMAIL PROTECTED] L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50 B.P.52627 - 31326 CASTANET TOLOSAN Cedex - FRANCE --

Re: [base] Workaround for upgrading a Postgres database

> ALTER TABLE "Features" DROP CONSTRAINT "Features_uniquecoordinate" > > /Nicklas > OK Done. Thanks a lot. -- Emmanuel COURCELLE[EMAIL PROTECTED] L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50 B.P.52627 - 31326

Re: [base] Workaround for upgrading a Postgres database

actJdbc2Statement.java:286) at com.mchange.v2.c3p0.impl.NewProxyStatement.executeUpdate(NewProxyStatement.java:64) at net.sf.basedb.core.HibernateUtil.dbIndexes(HibernateUtil.java:1715) ... 1 more Is it serious ? -- Emmanuel COURCELLE[EMAIL PROTECTED] L.I.P.M. (UMR CNRS

[base] updating to Base 2.1 with postgresql

is there anything else wrong ? Is there anything I can do to upgrade anyway (is it required running this script to upgrade to 2.1 ?) Thanks in advance for your advices. -- Emmanuel COURCELLE[EMAIL PROTECTED] L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50 B.P.52627