launching BayesNet module from MEV

Help
2009-02-23
2013-05-20
  • mudita singhal

    mudita singhal - 2009-02-23

    Hi,

    I have a very basic question. I am trying to launch the BayesNet interface from MEV v4.3.01 on a windows XP machine. If I dont have a dataset loaded into it, I see the Bayesian Network button disabled under the Miscellaneous options. if I load a dataset so that the Miscellaneous option and the Bayesian Network buttons comes enabled, I get a message saying "Organism and/or array information unavailable.

    Help!
    Mudita

     
    • raktim

      raktim - 2009-02-24

      Hello Mudita,

      The BayesNet module needs Organism and Chip info to use correct annotation data to run. What microarray are you using? Maybe we already provide the annotation for that platform. When you load your data,  try to select the organism and the corresponding array, that should solve the problem.

      If you don't see you array in the drop down list, it means we currently do not have annotation for the chip type. We keep adding new array annotation frequently.
      Hope it helps,
      Raktim

       
      • mudita singhal

        mudita singhal - 2009-02-24

        Hi Raktim,

        Thanks for your reply. I am trying to use the sample data provided in the data directory with MEV and have tried different options. I have also downloaded the BN data pointed out in the appendix section of the manual. Still cannot get to the BN interface. Can you point me to the sample data file and the organism name and array file to use, which will make the BN interface button enabled? Incase it helps, the following is the trace of the error I see:

        MultiExperimentViewer - version 4.3 - Windows XP
        Java Runtime Environment version: 1.6.0_07
        Java Runtime Environment vendor: Sun Microsystems Inc.
        Java Virtual Machine name: Java HotSpot(TM) Client VM
        Java Virtual Machine version: 10.0-b23
        Java Virtual Machine vendor: Sun Microsystems Inc.
        Java 3D Runtime Environment: Java 3D Core Runtime Environment
        Java 3D Runtime Environment vendor: Sun Microsystems, Inc.
        Java 3D Runtime Environment version:1.2
        Operating System name: Windows XP
        Operating System version: 5.1
        Operating System architecture: x86
        Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
                at org.tigr.microarray.mev.file.StanfordFileLoader.processStanfordFile(S
        tanfordFileLoader.java:415)
                at org.tigr.microarray.mev.file.StanfordFileLoader$StanfordFileLoaderPan
        el.onBrowse(StanfordFileLoader.java:647)
                at org.tigr.microarray.mev.file.StanfordFileLoader$StanfordFileLoaderPan
        el$EventListener.actionPerformed(StanfordFileLoader.java:686)
                at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
                at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
                at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
                at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
                at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Sour
        ce)
                at java.awt.Component.processMouseEvent(Unknown Source)
                at javax.swing.JComponent.processMouseEvent(Unknown Source)
                at java.awt.Component.processEvent(Unknown Source)
                at java.awt.Container.processEvent(Unknown Source)
                at java.awt.Component.dispatchEventImpl(Unknown Source)
                at java.awt.Container.dispatchEventImpl(Unknown Source)
                at java.awt.Component.dispatchEvent(Unknown Source)
                at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
                at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
                at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
                at java.awt.Container.dispatchEventImpl(Unknown Source)
                at java.awt.Window.dispatchEventImpl(Unknown Source)
                at java.awt.Component.dispatchEvent(Unknown Source)
                at java.awt.EventQueue.dispatchEvent(Unknown Source)
                at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
                at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
                at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
                at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
                at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
                at java.awt.EventDispatchThread.run(Unknown Source)
        java.lang.NullPointerException
                at org.tigr.microarray.mev.file.AnnotationDownloadHandler.onClickAnnDown
        load(AnnotationDownloadHandler.java:229)
                at org.tigr.microarray.mev.file.AnnotationDownloadHandler$EventListener$
        1.run(AnnotationDownloadHandler.java:300)
                at java.lang.Thread.run(Unknown Source)
        java.lang.NullPointerException
                at org.tigr.microarray.mev.file.AnnotationDownloadHandler.onClickAnnDown
        load(AnnotationDownloadHandler.java:229)
                at org.tigr.microarray.mev.file.AnnotationDownloadHandler$EventListener$
        1.run(AnnotationDownloadHandler.java:300)
                at java.lang.Thread.run(Unknown Source)

         
    • Eleanor Howe

      Eleanor Howe - 2009-02-25

      Hi Mudita,

      I think this error is a result of one or more blank lines in your input data file. Can you try removing any blank lines from your file using a text editor and let me know if that works? Keep in mine that the blank line could be the very last line of the file.

      Eleanor

       
      • mudita singhal

        mudita singhal - 2009-02-25

        Hi Eleanor,

        I doubt this is a problem with the data file since I have tried many different files and have gone back and checked and they do not have blank lines. For instance I tried using the expression data file "affy_U133plus2_dataset.txt" from the sample data directory that comes with an MEV installation. I selected the U133A array type and Human as the organism name. The data loaded fine but it still does not show me the BayesNet interface.

        Thanks
        Mudita

         
    • Eleanor Howe

      Eleanor Howe - 2009-02-25

      Hi Mudita,

      Ok, so maybe it's not a problem with blank lines. But it's definitely something wrong with how the file is loading, because that stack trace you sent me is coming from the file loader section of MeV.

      When you loaded your file, after you selected your species name and array name, did you click the button to the right of those drop-down menus? It should be labeled either "Download" or "Select". If you don't click that button, MeV won't download your annotation.

      Eleanor

       
      • mudita singhal

        mudita singhal - 2009-02-25

        Thanks Eleanor. It helped. But i had to load the same annotation twice (by first selecting the download button and then clicking on the select button) before I could see the BN interface.

         

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