Oct 1, 2015, 1:23:03 PM (6 years ago)
Nicklas Nordborg

References #1941: Store experimental factor values as part experiments

Updated documentation and screen shots related to the new functionality.

1 edited


  • trunk/doc/src/docbook/user/experiments.xml

    r5800 r6961  
    291291        To be able to use the values of the experimental factors
    292292        in the analysis of your data the values must be accessible
    293         from the raw bioassays. Since most of your annotations are
    294         probably made at the sample or biosource level the raw bioassays
    295         must inherit those annotations.
    296         <nohelp>Read <xref linkend="annotations.inheriting" />
    297         for more information about this.</nohelp>
    298       </para>
     293        from the <guilabel>root raw bioassays</guilabel>. A root raw bioassay
     294        is a wrapper around a raw bioassay that is part of the experiment and
     295        it has two purposes:
     296      </para>
     298      <itemizedlist>
     299        <listitem>
     300          <para>
     301          Hold experimental factor values for the raw bioassay in the
     302          context of the current experiment without affecting other
     303          experiments were the same raw bioassay is used.
     304          </para>
     305        </listitem>
     306        <listitem>
     307          <para>
     308          Give the owner of the experiment control over the experimental factor
     309          values used. In a multi-project setting this is important since the
     310          owner of the raw bioassay may not permit changes to the raw bioassay.
     311          Use the <guilabel>clone</guilabel> feature when inheriting
     312          annotations to the root raw bioassay to make sure that downstream
     313          analysis is not affected by changes made to the original parent
     314          annotations (unless you do a manual <guilabel>resync</guilabel>).
     315          </para>
     316        </listitem>
     317      </itemizedlist>
     319      <para>
     320        Since most of your annotations are probably made at the sample or biosource
     321        level the root raw bioassays must inherit or clone those annotations.
     322        The experiment view page lists all experimental factors and their current
     323        values for each root raw bioassay.
     324      </para>
     326      <para>
     327        There is a quick access to the <link linkend="annotations.batch-inherit">batch inherit</link>
     328        function that makes it easy to inherit any annotations that are missing.
     329        <nohelp>See also <xref linkend="annotations.inheriting" /> for more information about inheriting annotations.</nohelp>
     330      </para>
     332      <nohelp>
     333      <figure id="experiments_analysis.figures.experiment_factor_values">
     334        <title>Experimental factor values</title>
     335        <screenshot>
     336          <mediaobject>
     337            <imageobject><imagedata
     338              fileref="figures/experiment_factor_values.png" format="PNG"
     339              /></imageobject>
     340          </mediaobject>
     341        </screenshot>
     342      </figure>
     343      </nohelp>
    300345      <tip>
    301346        <para>
Note: See TracChangeset for help on using the changeset viewer.