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Christin
2010-04-16
2013-05-20
  • Christin
    Christin
    2010-04-16

    I have a problem loading script files.

    In the simplest example I only have one algorithm, HCL, and I execute and save the script successfully. However, when trying to load the script again I get a validation error saying that the distance function has an "Incorrect value type" eventhough the value is "4" and should be an integer between 0 and 9. I have tried different integers and also HCL with support tree but get the same result when I try to load the script.

    Any clues?

     
  • Eleanor Howe
    Eleanor Howe
    2010-04-16

    Hi there,

    I've tried replicating this error, but I'm not able to. I also created a new script with only one algorithm, HCL, and was able to execute, save and re-load it.

    Can you tell me what version of MeV you are using and what system your are running it on? It may help if you send me your script, also. You can just paste it into this forum or send me an email to my sourceforge account.

    Eleanor

     
  • Christin
    Christin
    2010-04-18

    Hi!

    I'm running MeV 4_5_1 on Windows Vista. My expression data contains several samples (columns) and genes (rows). Below I have pasted a simple script that runs when I create it, but I cannot reload it. I'm completely new to MeV so I'm sure there's a trivial explanation that I'm hoping you'll be able to provide…

    Cheers,
    Christin

    <?xml version="1.0"?>
    <!DOCTYPE TM4ML SYSTEM "C:\Users\christin\.mev\mev_script_dtd.dtd">
    <TM4ML version="1.0">
       <mev version="1.0">
          <!- Original Script Creation Date: Apr 18, 2010 7:43:21 PM ->

          <!- Script Name: Test ->

          <!- Script Description: A test ->

          <primary_data id="1"/>
          <analysis>
             <alg_set input_data_ref="1" set_id="1">
                <algorithm alg_id="1" alg_name="HCL" alg_type="cluster" input_data_ref="1">
                   <plist>
                      <param key="optimize-sample-ordering" value="true"/>
                      <param key="distance-absolute" value="false"/>
                      <param key="calculate-genes" value="true"/>
                      <param key="calculate-experiments" value="true"/>
                      <param key="method-linkage" value="1"/>
                      <param key="distance-factor" value="1.0"/>
                      <param key="distance-function" value="4"/>
                      <param key="optimize-gene-ordering" value="true"/>
                   </plist>
                   <output_data output_class="single-output">
                      <data_node data_node_id="2" name="Single Ordered Output"/>
                   </output_data>
                </algorithm>
             </alg_set>
          </analysis>
       </mev>
    </TM4ML>

     
  • Christin
    Christin
    2010-04-19

    Hi again,

    Some further investigations has revealed that the offending lines are:

    <param key="optimize-sample-ordering" value="true"/>
    <param key="optimize-gene-ordering" value="true"/>

    Is there something wrong with the explicit syntax of the lines, or must they appear in a particular order?

    Cheers,
    Christin

     
  • Eleanor Howe
    Eleanor Howe
    2010-04-19

    Hi Christin,

    Congratulations, on your first try, you've found a bug in MeV! We've put a bugfix into our development branch and will release it with the next version,due out in July. In the meantime, you should be able to make the script work by removing those two lines from it. I'm afraid that means the script won't be able to do the node order optimization automatically, though.

    I would be careful using those options anyways, by the way. They take a lot of time and a lot of memory - that's why they're off by default.

    Eleanor

     
  • Christin
    Christin
    2010-04-20

    Hi Eleanor!

    Well, since I'm a tester by profession I guess that's only fair :) Thanks for your reply, I'll keep running my scripts without these options and wait for the next release (and I do really appreciate the possibility to use scripts!).

    Cheers,
    Christin