source: trunk/doc/src/docbook/userdoc/experiments.xml @ 3318

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<sect1 id="experiments_analysis.experiments">
  <title>Experiments</title>
  <para>TODO</para>

  <sect2 id="experiments_analysis.experiment.properties">
    <title>Experiment properties</title>
    
    <para>TODO</para>
    
  </sect2>
  
  <sect2 id="experiments_analysis.experiment.overview">
    <title>Experiment overview</title>
    
    <para>
      With the <guilabel>Experiment overview</guilabel> 
      function you can get an overview of all hybridizations,
      extracts, samples, annotations, etc. used in an 
      experiment. The overview includes a lot of checks
      that validates your experimental setup for missing
      or possibly incorrect information.
    </para>
    
    <para>
      You can access the overview of an experiment by navigating
      to the single-item view of the experiment you are interested in.
      Then, switch to the <guilabel>Overview</guilabel> tab that
      is present on that page. Here is an example of what is displayed:
    </para>
    
    <figure id="experiments_analysis.figures.experimentoverview">
      <title>The experiment overview</title>
      <screenshot>
        <mediaobject>
          <imageobject><imagedata 
            fileref="figures/experiment_overview.png" format="PNG"
            /></imageobject>
        </mediaobject>
      </screenshot>
    </figure>
    
    <helptext external_id="experiment.overview " 
      title="Experiment overview">
    <para>
      The page is divided into three sections:
    </para>
    
    <itemizedlist>
      <listitem>
        <para>
        To the left is a tree displaying all items
        in the experiment and how they are linked to
        each other.
        </para>
      </listitem>
      
      <listitem>
        <para>
        The lower right shows a list of warnings and error
        messages that was found when validating the experiment.
        <nohelp>
        In the example you can see that we have failed to
        specify a value for the <guilabel>Temperature</guilabel>
        protocol parameter for one of the samples.
        </nohelp>
        </para>
      </listitem>
        
      <listitem>
        <para>
          The upper right shows information about the
          currently selected item in the tree. This part also
          contains more information errors or warnings for this
          item. It may also present you with one or more suggestions
          about how to fix the problem and with a link that
          takes you to the most probable location where you can fix
          the error or warning.
        </para>
        
        <note>
          <title>No links?</title>
          If you don't have permission to change things no links
          will be shown.
        </note>
        
      </listitem>
        
    </itemizedlist>
    
    <seeother>
      <other external_id="experiment.overview.validationoptions"
        >Validation options</other>
      <other external_id="experiment.overview.fixfailures"
        >How to fix validation failures</other>
    </seeother>
    
    </helptext>
    
    <sect3 id="experiments_analysis.validationoptions">
      <title>Validation options</title>
      <para>
        Click on the <guibutton>Validation options</guibutton>
        button in the toolbar to open the <guilabel>Validation
        options</guilabel> dialog.
      </para>
      
      <figure id="experiments_analysis.figures.validationoptions">
        <title>Validation options</title>
        <screenshot>
          <mediaobject>
            <imageobject><imagedata 
              fileref="figures/validation_options.png" format="PNG"
              /></imageobject>
          </mediaobject>
        </screenshot>
      </figure>         
      
      <helptext external_id="experiment.overview.validationoptions" 
        title="Validation options">
        <para>
          The validation procedure is highly 
          configurable and you can select what you want to
          ignore, or something should be displayed as an error
          or warning.
        </para>
        
        <variablelist>
          <varlistentry>
            <term>
            <indexterm><primary>Presets</primary><secondary>experiment validation</secondary></indexterm>
            <guilabel>Presets</guilabel></term>
            <listitem>
              <para>
              The list contains predefined and
              user defined validation options.
              Use the <guibutton>Save as&hellip;</guibutton>
              button to save the current options as a user defined
              preset. The <guibutton>Remove&hellip;</guibutton>
              button is used to remove the currently selected
              preset. Predefined presets can't be deleted.
              </para>
            </listitem>
          </varlistentry>
          
          <varlistentry>
            <term><guilabel>Project defaults</guilabel></term>
            <listitem>
              <para>
              The options in this section are used to check
              if your experiment uses the same values as set
              by the project default values of the currently active
              project<nohelp>
              (see <xref linkend="project_permission.projects" />)</nohelp>. 
              If no project is active or if the active project doesn't
              have default values these options are ignored.
              </para>
            </listitem>
            
          </varlistentry>
          
          <varlistentry>
            <term><guilabel>Missing items</guilabel></term>
            <listitem>
              <para>
              The options in this section are used to check if
              you have specified values for optional items. 
              For example, there is an option that warns you if 
              you havn't specified a protocol.
              </para>
            </listitem>
          </varlistentry>
          
          <varlistentry>
            <term><guilabel>Annotations</guilabel></term>
            <listitem>
              <para>
              The options in this section are used to check 
              problems related to annotations. The most
              important ones are listed here:
              </para>
              
              <itemizedlist>
              <listitem>
                <simpara>
                <emphasis>Missing MIAME annotation value</emphasis>:
                Checks that you have specified values
                for all annotations marked as 
                <guilabel>Required for MIAME</guilabel>.
                </simpara>
              </listitem>
              
              <listitem>
                <simpara>
                <emphasis>Missing factor value</emphasis>:
                Checks that you have specified values for
                all annotations used as experimental factors in
                the experiment.
                </simpara>
              </listitem>
              
              <listitem>
                <simpara>
                <emphasis>Missing parameter value</emphasis>:
                Checks that you have specified values
                for all protocol parameters.
                </simpara>
              </listitem>

              <listitem>
                <simpara>
                <emphasis>Annotation is protocol parameter</emphasis>:
                Checks if an item has been annotated with a 
                an annotation that is actually a protocol parameter.
                </simpara>
              </listitem>

              <listitem>
                <simpara>
                <emphasis>Annotation has invalid value</emphasis>:
                Checks if annotation values are correct with 
                respect to the rules given by the annotation type.
                This might include numeric values that are outside 
                the valid range, or values not in the list
                of allows values for an enumerated annotation type.
                </simpara>
              </listitem>

              <listitem>
                <simpara>
                <emphasis>Inheriting annotation from non-parent</emphasis>:
                Checks if inherited annotations really comes from a
                parent item. This might happen if you rearrange 
                parent-child relationship because you found that
                they were incorrectly linked.
                </simpara>
              </listitem>
              </itemizedlist>
              
            
            </listitem>
          </varlistentry>
          
          <varlistentry>
            <term><guilabel>Denied access</guilabel></term>
            <listitem>
              <para>
              The options in this section are used to
              check if you don't have access (read permission)
              to an item in the experiment hierarchy. If this 
              happens the validation can't proceed in that branch.
              This might mask other validation problems.
              </para>
            </listitem>
          </varlistentry>
          
          <varlistentry>
            <term><guilabel>Other</guilabel></term>
            <listitem>
              <para>
              This section collects options that doesn't fit
              into any of the other sections. The most
              important options are:
              </para>
              
              <itemizedlist>
                <listitem>
                  <simpara>
                  <emphasis>Array deign mismatch</emphasis>:
                  Checks if the array design specified for
                  a raw bioassay is the same array design
                  specified for the hybridization.
                  </simpara>
                </listitem>
                
                <listitem>
                  <simpara>
                  <emphasis>Multiple array designs</emphasis>:
                  Checks if all raw bioassays use the
                  same array design or not.
                  </simpara>
                </listitem>
              
                <listitem>
                  <simpara>
                  <emphasis>Incorrect number of labled extracts</emphasis>:
                  Checks if the number of labeled extracts
                  match the number of channels for the experiment.
                  </simpara>
                </listitem>

                <listitem>
                  <simpara>
                  <emphasis>Non-unique name</emphasis>:
                  Checks if two items of the same type
                  have the same name. A unique name if important
                  when exporting data in Tab2Mage format.
                  </simpara>
                </listitem>

                <listitem>
                  <simpara>
                  <emphasis>Circular reference to pooled item</emphasis>:
                  If you have used pooling, checks that no 
                  circular references have been created.
                  </simpara>
                </listitem>
              
              </itemizedlist>
              
            </listitem>
          </varlistentry>
          
        </variablelist>
        
        <para>
          Click on the <guibutton>Save</guibutton> button
          to use the current settings. The display will
          automatically refresh itself.
        </para>
        
      </helptext>
      
      <helptext external_id="experiment.overview.validationoptions.savepreset" 
        title="Save preset" webonly="1">
        
        <para>
        Saves all validation options as a preset. 
        </para>
        
        <variablelist>
          <varlistentry>
            <term><guilabel>Name</guilabel></term>
            <listitem>
              <para>
                The name of the preset. The name must be unique
                and if a preset with the same name already exists
                you will be asked if you want to overwrite it or not.
              </para>
            </listitem>
          </varlistentry>
        </variablelist>
        
        <para>
          Click on the <guibutton>Save</guibutton> button
          to save the preset or <guibutton>Cancel</guibutton>
          to abort.
        </para>
      </helptext>
      
    </sect3>
    
    <sect3 id="experiments_analysis.fixfailures">
      <title>Fixing validation failures</title>
      <helptext external_id="experiment.overview.fixfailures" 
        title="How to fix validation failures">
        
        <para>
        The experiment overview includes a function that allows
        you to quickly fix most of the problems found during the 
        validation. The easiest way to use the function is:
        </para>
        
        <orderedlist>
          <listitem>
            <simpara>
            Click on an error or warning in the list of failures in 
            the lower right
            pane. The tree in the left pane and the item overview in the
            top right pane will automatically be updated to show the
            exact location of the faulty item.
            </simpara>
          </listitem>
          <listitem>
            <simpara>
            The upper right pane should contain a list labeled
            <guilabel>Failure details</guilabel> with more information
            about each failure and also one or more suggestions for fixing
            the problem. For example, a failure due to a missing item
            should suggest that you add or select an item.
            </simpara>
          </listitem>
          
          <listitem>
            <simpara>
            The suggestions should also have links that takes
            you to an edit view where you can do the changes.
            </simpara>
          </listitem>
          
          <listitem>
            <simpara>
            After saving the changes you must click on the
            <guibutton>Revalidate</guibutton> button to update
            interface. If you want, you can fix more than one 
            failure before clicking on the button.
            </simpara>
          </listitem>
            
        </orderedlist>
      
      </helptext>
    </sect3>
    
  </sect2>
  
  <sect2 id="experiments_analysis.magexport">
    <title>Tab2Mage export</title>
    <para>TODO</para>
  </sect2>

</sect1>