[Nelsonlab-cmts] dev-boconnor/project_logic_analysis/conf original_glioma_classification_with_vgl.xml,1.2,1.3 original_glioma_vgl_parsing_pipe.xml,1.2,1.3

[<boc...@su...>]

Update of /cvsroot/dev-boconnor/project_logic_analysis/conf
In directory sumo.genetics.ucla.edu:/tmp/cvs-serv4067

Modified Files:
	original_glioma_classification_with_vgl.xml 
	original_glioma_vgl_parsing_pipe.xml 
Log Message:
I did a code review on these modules to make sure the performance I'm seeing with VGL is correct.  I found some bugs, specifically in the 1A category (due to a problem with the VGL output format) and also with the mean of the category being used rather than the other categories means.  These problems have been fixed yet the performance looks the same if not a little worse.


Index: original_glioma_classification_with_vgl.xml
===================================================================
RCS file: /cvsroot/dev-boconnor/project_logic_analysis/conf/original_glioma_classification_with_vgl.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** original_glioma_classification_with_vgl.xml	23 Feb 2006 22:11:58 -0000	1.2
--- original_glioma_classification_with_vgl.xml	28 Feb 2006 07:41:06 -0000	1.3
***************
*** 33,37 ****
          </output>
        </step>
!       <step id="48.4" active="0" type="shell_command" processor="R">
          <processor_args>
            <arg id="1" name="" value="--vanilla"/>
--- 33,37 ----
          </output>
        </step>
!       <step id="48.4" active="1" type="shell_command" processor="R">
          <processor_args>
            <arg id="1" name="" value="--vanilla"/>

Index: original_glioma_vgl_parsing_pipe.xml
===================================================================
RCS file: /cvsroot/dev-boconnor/project_logic_analysis/conf/original_glioma_vgl_parsing_pipe.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** original_glioma_vgl_parsing_pipe.xml	23 Feb 2006 22:11:58 -0000	1.2
--- original_glioma_vgl_parsing_pipe.xml	28 Feb 2006 07:41:06 -0000	1.3
***************
*** 7,11 ****
                    way around this would be for Marc to alter the output so the summary columns are in a fixed position.
          -->
!       <step id="30.2" active="0" type="module" processor="Nelson::Pipe::Container::Job::ReadVGLOutput">
          <input>
            <item id="profile_output_dir" value="data/[% datadir %]/vgl"/>
--- 7,11 ----
                    way around this would be for Marc to alter the output so the summary columns are in a fixed position.
          -->
!       <step id="30.2" active="1" type="module" processor="Nelson::Pipe::Container::Job::ReadVGLOutput">
          <input>
            <item id="profile_output_dir" value="data/[% datadir %]/vgl"/>