[base] How can I associate Illumina data with hybs (and samples)

[vegard nygaard]

Hi I am testing out the Illumina importer and have some questions.

Can I connect the created raw bioassays to hybridizations (and indirectly to
samples)?  On the scan page I looked for a associate raw bioassay , but
only found the new raw bioassay. In order for the importer to be really
useful I need to connect the raw data to samples in some way. From reading
earlier posts it seems that connecting all the raw bioassays to one single
scan is possible, but will there in upcoming base versions be more flexible
association possibilities?

If the Illumina Importer cannot attach raw bioassays to samples I wonder if
I can use the Tab2Mage Importer or BatchDataImporter with Illumina data?


Best regards.
Vegard Nygaard
Software Engineer
Department of Tumor Biology (Montebello)
Rikshospitalet-Radiumhospitalet Medical Center 0310 Oslo
Bioinformatics user support (NMC)
Phone 0047 22935590



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Re: [base] BASE2 login error

[Nicklas Nordborg]

Reha Yildirimman wrote:
 Hello,
 
 I have the following setup:
 BASE2.4.0
 tomcat 5.5.17
 mysql 5.0.45
 64bit linux system
 

The error seems to be related to the Recently view items menu. For 
some reason the string that holds the information has become corrupt and 
the code is unfortunately not able to handle this. The best advice I can 
give right now is to edit the basedir/www/include/menu.jsp to try to 
avoid the error. It is line 110 in this file that is causing the error.

A temporary solution might be to change this to something like:
int itemId = tmp.length  2 ? 0 : Values.getInt(tmp[1], 0);

I'll try to check in a better fix in subversion tomorrow.

/Nicklas

 Without changing anything, today I get the following error when I try to 
 login:
 
 java.lang.ArrayIndexOutOfBoundsException: 1
at org.apache.jsp.include.menu_jsp._jspService(menu_jsp.java:185)
at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
at 
 org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:332)
  
 
at 
 org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314)
at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
at 
 org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
  
 
at 
 org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
  
 
at 
 org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672)
  
 
at 
 org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:574)
  
 
at 
 org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:499)
  
 
at 
 org.apache.jasper.runtime.JspRuntimeLibrary.include(JspRuntimeLibrary.java:966)
  
 
at 
 org.apache.jasper.runtime.PageContextImpl.include(PageContextImpl.java:614)
at net.sf.basedb.clients.web.taglib.Body.doStartTag(Body.java:293)
at 
 org.apache.jsp.exception.exception_jsp._jspService(exception_jsp.java:173)
at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
at 
 org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:332)
  
 
at 
 org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314)
at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
at 
 org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
  
 
at 
 org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
  
 
at 
 org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672)
  
 
at 
 org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:465)
  
 
at 
 org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:398)
  
 
at 
 org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
  
 
at 
 org.apache.catalina.core.StandardHostValve.custom(StandardHostValve.java:363) 
 
at 
 org.apache.catalina.core.StandardHostValve.throwable(StandardHostValve.java:212)
  
 
at 
 org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:134) 
 
at 
 org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105) 
 
at 
 org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
  
 
at 
 org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
at 
 org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)
at 
 org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(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 java.lang.Thread.run(Thread.java:595)
 
 
 I restarted everything, dropped and updated the dbindex wihtout a 
 change. I can access the mysql database and tomcat is working.
 The BASE2 frontpage is shown, when I put a wrong password I get the 
 appropriate error message and clicking on More about this server opens
 the pop-window with all the info (version, etc.) - just enterning the 
 correct password results in the above error message
 
 Does anybody have encountered this or might have a clue what is going 
 (or not going) on ?
 
 Many thanks in advance for your help.
 
 Cheers,
 
 Reha
 
 

Re: [base] How can I associate Illumina data with hybs (and samples)

[Nicklas Nordborg]

vegard nygaard wrote:
 Hi I am testing out the Illumina importer and have some questions.
 
 Can I connect the created raw bioassays to hybridizations (and indirectly to
 samples)?  

Yes. When you run the importer you have the option to select a scan that 
will be associated with the raw bioassays. The scan can be associated 
with a hybridization which is then associated with labeled extracts, and 
so on, up to samples.

  On the scan page I looked for a associate raw bioassay , but
 only found the new raw bioassay. 

You can select which scan a raw bioassay belongs to from the Edit 
rawbioassay page.

  In order for the importer to be really
 useful I need to connect the raw data to samples in some way. From reading
 earlier posts it seems that connecting all the raw bioassays to one single
 scan is possible, but will there in upcoming base versions be more flexible
 association possibilities?

We have discussed this and came to the conclusion that the current 
implementation is the most accurate representation of the process. The 
BASE model assumes that there is a one-to-one relation between a slide 
and hybridization. An Illumina slide has several (8 or more) arrays on a 
single slide. This doesn't fit the current model in all aspects. Some 
compromises has to be made. This is how we decided to do:

  * The slide is represented a single ArraySlide item in the database
  * The hybridization event links 8 (or more) labeled extracts to
the slide (one for each array)
  * A single scan event represents the scanning
  * One raw bioassay for each array is created

This will make is possible to accurately record scan and hybridization 
parameters without having to duplicate (8 times) the same data. The 
drawback is that the experiment validation will complain about the 8 
labeled extracts since it expects only 1 for 1-channel data. It will 
also complain about all labeled extracts having the same label. But 
these warnings can be turned off. Another drawback is that all 8 labeled 
extracts will be treated as parents to all 8 raw bioassays, even though 
there really is a one-to-one relationship between those.

/Nicklas

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