Nov 7, 2006, 11:35:35 AM (16 years ago)
Jari Häkkinen

More getting started information.

1 edited


  • trunk/doc/user/getting_started.html

    r2841 r2869  
    2828  <head>
    29     <title>BASE 2.0 - User documentation: Getting started</title>
     29    <title>BASE 2.1 - User documentation: Getting started</title>
    3030    <link rel=stylesheet type="text/css" href="../styles.css">
    3131  </head>
    4040    </div>
    42     <h1>BASE 2.0 - User documentation: Getting started</h1>
     42    <h1>BASE 2.1 - User documentation: Getting started</h1>
    4444    <div class="abstract">
    230230          <li>
    231231            <p> (Affymetrix only) <b>Install
    232             <a
     232            <a name=RMAExpressInstall
    233233            href=http://baseplugins.thep.lu.se/wiki/thep.lu.se.RMAExpress>RMAExpress
    234234            plug-in for BASE</a></b> <br> This plug-in is required for
    337337        bioassay. You can leave the rest untouched. Redo for all raw
    338338        data files. (Yes a batch creator would be nice.) </p>
    339       <li>
     339      </li>
    341341      <li>
    347347      </li>
     349      <li>
     350        <p> <b>Analysing an experiment step I</b> <br> Select the
     351        newly created experiment and in the the experiment windown
     352        select the 'Bioassay sets' tab. There are no bioassay sets and
     353        you must create a root bioassay set. This step is different
     354        depending on what data is used in the experiment but note that
     355        this paragraph ends with information valid for all type of
     356        data. </p>
     358        <p> <i>Affymetrix</i> <br> Click on the 'New root bioassay set
     359        ...' tab and select the RMAExpress plug-in in the pop up. (If
     360        the plug-in does not appear as an option, the installation of
     361        the plug-in has failed. Please refer
     362        to <a href=#RMAExpressInstall>Installing RMAExpress plug-in
     363        for BASE</a>.) Click on the 'Next' button and in the new
     364        window set the name for the bioassay set and select the
     365        bioassays you want to include for this analysis. Click
     366        'Next'. In the next pop up you can change information if you
     367        like but it is not necessary, when done click on 'Finish' to
     368        add the analysis job to the job queue. The job will start
     369        automatically when the server as an open slot for it. The last
     370        pop up window will report progress on the job. </p>
     372        <p> <i>All flavours</i> <br> You can safely close the job
     373        progress window, the server will run the job anyway. If you
     374        want to monitor the progress of the job after closing the job
     375        window just go to 'View' -> 'Jobs' and locate your job in the
     376        list and select it. When the job is done the new bioassay set
     377        will be added to the list of bioassay set for the
     378        experiment. Unfortunately the list does not auto update so you
     379        need to click on the 'Properties' tab and the on the 'Bioassay
     380        sets' tab to refresh the list of bioassay sets. </p>
     381      </li>
     383      <li>
     384        <p> <b>Analysing an experiment step II</b> <br> Now you should
     385        have the first bioassay set. In the list of bioassay sets you
     386        will have a number of icons attached that will start
     387        tools. The set of tools available for bioassay sets is context
     388        sensitive, <i>i.e.</i>, only tools that can handle the
     389        bioassay sets are shown. At the time of writing of this
     390        document there are four icons available; A simple plot tool,
     391        experiment explorer, a filtering tool, and a plug-in
     392        runner. You have to try these on your own. The aim with this
     393        paragraph is to highlight the fact that you can export the
     394        bioassay set data for use outside BASE. </p>
     396        <p> To export bioassay set data select a bioassay set. In the
     397        bioassay set presentation window you will have an export
     398        button just below the tabs on the top. (There is also an
     399        export button for the Sub analysis tree which may be confusing
     400        at first, but his button will export information about the
     401        analysis tree.) So, assuming you select the proper export
     402        button you will be given a list of different export
     403        formats. The list of supported eports depends on what plug-ins
     404        are added to the server, but there should at least be an
     405        export to <a href=http://www.tm4.org/mev.html>MultiExperiment
     406        Viewer</a> maintained by the Dana Farber Cancer Institute. </p>
     407      </li>
    349409      </ol>
    351411    </ol>
     413    <p> This concludes this short document on how to get going with
     414    BASE. We have not covered how to use the LIMS part of BASE, nor
     415    annotations, and much more. We are creating documentation, please
     416    browse <a href=http://base.thep.lu.se/>BASE web site</a> for the
     417    latest available documents. </p>
    353419  </body>
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