Changeset 3362


Ignore:
Timestamp:
May 22, 2007, 12:11:05 PM (14 years ago)
Author:
Nicklas Nordborg
Message:

References #546: Added some information about experiments

File:
1 edited

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

    r3318 r3362  
    2929<sect1 id="experiments_analysis.experiments">
    3030  <title>Experiments</title>
    31   <para>TODO</para>
     31  <para>
     32    Experiments are the starting point for analysis. When you have
     33    uploaded and imported your raw data, collected and registered all
     34    information and annotations about samples, hybridizations, and other
     35    items, it is time to collect everything in an experiment.
     36  </para>
     37 
     38  <para>
     39    To create a new experiment you can either mark one ore more
     40    raw biossays on the raw bioassays list view and use the
     41    <guibutton>New experiment</guibutton> button. You can also
     42    create a new experiment from the experiments list view.
     43  </para>
    3244
    3345  <sect2 id="experiments_analysis.experiment.properties">
    3446    <title>Experiment properties</title>
    3547   
    36     <para>TODO</para>
     48    <figure id="experiments_analysis.figures.experiment_properties">
     49      <title>Create experiment</title>
     50      <screenshot>
     51        <mediaobject>
     52          <imageobject><imagedata
     53            fileref="figures/experiment_properties.png" format="PNG"
     54            /></imageobject>
     55        </mediaobject>
     56      </screenshot>
     57    </figure>         
     58   
     59   
     60    <helptext external_id="experiment.edit" title="Edit experiment">
     61   
     62      <variablelist>
     63      <varlistentry>
     64        <term><guilabel>Name</guilabel></term>
     65        <listitem>
     66          <para>
     67            The name of the experiment.
     68          </para>
     69        </listitem>
     70      </varlistentry>
     71     
     72      <varlistentry>
     73        <term><guilabel>Raw data type</guilabel></term>
     74        <listitem>
     75          <para>
     76            The raw data type to use in the experiment. All raw bioassays
     77            must have raw data with this type.
     78          </para>
     79        </listitem>
     80      </varlistentry>
     81
     82      <varlistentry>
     83        <term><guilabel>Directory</guilabel></term>
     84        <listitem>
     85          <para>
     86            A directory in the BASE file system where plug-ins
     87            can save files that are generated during the analysis.
     88            This is optional and if not given the plug-ins must ask
     89            about a directory each time they need it. Use the
     90            <guibutton>Select</guibutton> button to browse the file system
     91            or create a new directory.
     92          </para>
     93        </listitem>
     94      </varlistentry>
     95     
     96      <varlistentry>
     97        <term><guilabel>Raw bioassays</guilabel></term>
     98        <listitem>
     99          <para>
     100            The raw bioassays you want to analyze in this experiment. If
     101            you created the experiment from the raw bioassays list the
     102            selected raw bioassays are already filled in. Use the
     103            <guibutton>Add raw bioassays</guibutton> button to add more
     104            raw bioassays or the <guibutton>Remove</guibutton> button
     105            to remove the selected raw bioassays from the list.
     106          </para>
     107        </listitem>
     108      </varlistentry>
     109     
     110      <varlistentry>
     111        <term><guilabel>Description</guilabel></term>
     112        <listitem>
     113          <para>
     114            A description of the experiment.
     115          </para>
     116        </listitem>
     117      </varlistentry>
     118
     119      </variablelist>
     120     
     121      <para>
     122        Click on the <guibutton>Save</guibutton> button to save the
     123        changes or on <guibutton>Cancel</guibutton> to abort.
     124      </para>
     125     
     126      <seeother>
     127        <other external_id="experiment.edit.publication">Publication</other>
     128        <other external_id="experiment.edit.factors">Experimental factors</other>
     129      </seeother>
     130    </helptext>
     131   
     132    <sect3 id="experiments_analysis.experiment.publication">
     133      <title>The publication tab</title>
     134     
     135      <helptext external_id="experiment.edit.publication"
     136        title="Experiment publication">
     137
     138        <para>
     139          On this tab you can enter information about a publication
     140          that is the result of the experiment. All of this information
     141          is optional.
     142        </para>
     143       
     144        <variablelist>
     145        <varlistentry>
     146          <term><guilabel>PubMedId</guilabel></term>
     147          <listitem>
     148            <para>
     149              The ID of the publication in the
     150              <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query/static/overview.html"
     151                >PubMed</ulink> database.
     152            </para>
     153          </listitem>
     154        </varlistentry>
     155        <varlistentry>
     156          <term><guilabel>Title</guilabel></term>
     157          <listitem>
     158            <para>
     159              The title of the publication.
     160            </para>
     161          </listitem>
     162        </varlistentry>
     163        <varlistentry>
     164          <term><guilabel>Publication date</guilabel></term>
     165          <listitem>
     166            <para>
     167              The date the article was published. Use the
     168              <guibutton>Calendar</guibutton> button to select
     169              a date from a popup window.
     170            </para>
     171          </listitem>
     172        </varlistentry>
     173        <varlistentry>
     174          <term><guilabel>Abstract</guilabel></term>
     175          <listitem>
     176            <para>
     177              The article abstract.
     178            </para>
     179          </listitem>
     180        </varlistentry>
     181        <varlistentry>
     182          <term><guilabel>Experiment design</guilabel></term>
     183          <listitem>
     184            <para>
     185              An explanation of the experiment design.
     186            </para>
     187          </listitem>
     188        </varlistentry>
     189        <varlistentry>
     190          <term><guilabel>Experiment type</guilabel></term>
     191          <listitem>
     192            <para>
     193              A description of the experiment type.
     194            </para>
     195          </listitem>
     196        </varlistentry>
     197        <varlistentry>
     198          <term><guilabel>Affiliations</guilabel></term>
     199          <listitem>
     200            <para>
     201              Partners and other related organisations that
     202              have helped with the experiment.
     203            </para>
     204          </listitem>
     205        </varlistentry>
     206        <varlistentry>
     207          <term><guilabel>Authors</guilabel></term>
     208          <listitem>
     209            <para>
     210              The list of authors of the publication.
     211            </para>
     212          </listitem>
     213        </varlistentry>
     214        <varlistentry>
     215          <term><guilabel>Publication</guilabel></term>
     216          <listitem>
     217            <para>
     218              The body text of the publication.
     219            </para>
     220          </listitem>
     221        </varlistentry>
     222        </variablelist>
     223       
     224        <para>
     225          Click on the <guibutton>Save</guibutton> button to save the
     226          changes or on <guibutton>Cancel</guibutton> to abort.
     227        </para>
     228     
     229        <seeother>
     230          <other external_id="experiment.edit">Experiment properties</other>
     231          <other external_id="experiment.edit.factors">Experimental factors</other>
     232        </seeother>
     233      </helptext>
     234    </sect3>
    37235   
    38236  </sect2>
     237 
     238  <sect2 id="experiments_analysis.experiment.factors">
     239    <title>Experimental factors</title>
     240   
     241    <helptext external_id="experiment.edit.factors"
     242      title="Experimental factors">
     243   
     244      <para>
     245        The experimental factors of an experiment are the variables
     246        you are studying in the experiment. Typically the value of
     247        an experimental factor is varied between samples or group of samples.
     248        Different treatment methods is an example of an experimental factor.
     249      </para>
     250     
     251      <para>
     252        In the BASE world an experimental factor is the same as an annotation
     253        type. Since you probably have lots of annotations on your items that are not
     254        relevant for the experiment you must select the annotations types
     255        that should make up the experimental factors of the experiment.
     256      </para>
     257     
     258      <para>
     259        Use the <guibutton>Add annotation types</guibutton> button to
     260        select the annotation types that should be used as experimental
     261        factors. The <guibutton>Remove</guibutton> button removes the
     262        selected annotation types.
     263      </para>
     264
     265      <para>
     266        Click on the <guibutton>Save</guibutton> button to save the
     267        changes or on <guibutton>Cancel</guibutton> to abort.
     268      </para>
     269     
     270      <para>
     271        To be able to use the values of the experimental factors
     272        in the analysis of your data the values must be accessible
     273        from the raw bioassays. Since most of your annotations are
     274        probably made at the sample level the raw bioassays must
     275        inherit those annotations.
     276        <nohelp>Read <xref linkend="annotations" />
     277        for more information about this.</nohelp>
     278      </para>
     279     
     280      <tip>
     281        <para>
     282        Use the <guilabel>Experiment overview</guilabel> function to
     283        verify that all your raw bioassays has been annotated or
     284        inherited values for all experimental factors. If not, you
     285        should do that before starting with the analysis.
     286        </para>
     287      </tip>
     288     
     289      <seeother>
     290        <other external_id="experiment.edit">Experiment properties</other>
     291        <other external_id="experiment.edit.publication">Publication</other>
     292        <other external_id="experiment.overview">Experiment overview</other>
     293        <other external_id="annotations.edit.inerited">Inherit annotations</other>
     294      </seeother>
     295     
     296    </helptext>
     297  </sect2>
     298
    39299 
    40300  <sect2 id="experiments_analysis.experiment.overview">
     
    68328    </figure>
    69329   
    70     <helptext external_id="experiment.overview "
     330    <helptext external_id="experiment.overview"
    71331      title="Experiment overview">
    72332    <para>
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