Changeset 2810

Oct 26, 2006, 12:03:06 PM (17 years ago)
Jari Häkkinen

Improving getting started doc.

1 edited


  • trunk/doc/user/getting_started.html

    r2801 r2810  
    275275            box. Finalize with 'Save'. For Affymetrix the import is
    276276            done, whereas Genepix have to perform reporter map
    277             import. </p>
     277            import. Remember to share your designs (normally to group
     278            'Everyone'). </p>
    279280            <p> <i>Genepix reporter map import</i> <br> Click on the
    290291      </li>
     293      <p> A normal user is not allowed to add array design, reporter
     294      information, and a lot of other information to BASE. The reason
     295      for this is that a lot of information should only exist as one
     296      copy in the database. For example, reporters should only exist in
     297      one copy because everyone uses the same reporters. There is no
     298      need to store several copies of the same array design. </p>
     300      <p> A user will normally upload experimental data to BASE for
     301      import into the database. To be able to import the data, the
     302      array design used must be available in BASE at import time. If
     303      the array design is not available, a user with the proper
     304      credential must add the array design to BASE. </p>
     306      <ol type=a>
     308      <li>
     309        <p> <b> Create a new Project </b> <br> Go to 'View' ->
     310        'Projects' and click on the 'New...' tab. Name the project and
     311        save. In the projects listing page, click 'Set active' for the
     312        new project. The selected project should be displayed on top
     313        right as 'Active project'. Selecting an active project will
     314        influence the behaviour of BASE. Only information related to
     315        the active project will be displayed and items created will
     316        automatically be shared to the active project. </p>
     318        <p> The display of items shared to the active project only
     319        requires that the 'view/presets' pull-down menu options are
     320        properly set. In 'view/preset' you can select what should be
     321        displayed, and if only 'In current project' is selected then
     322        only information shared to a project will be shown. </p>
     323      </li>
     325      <li>
     326        <p> <b>Create raw bioassays</b> <br> Upload your raw data
     327        files. Go to 'View' -> 'Raw bioassays' and click on the
     328        'New...' tab. Name the raw bioassay. Select 'Raw data
     329        type'. Select the 'Array design', if you cannot see see
     330        designs in the pop-up the make sure that the 'view/presets'
     331        pull-down menu has 'Shared to me' marked and select appropriate
     332        design. Select 'CEL file' if you create an Affymetrix raw
     333        bioassay. You can leave the rest untouched. Redo for all raw
     334        data files. (Yes a batch creator would be nice.) </p>
     335      <li>
     337      <li>
     338        <p> <b>Create a new experiment</b> <br> Go to 'View' ->
     339        'Experiments' and click on the 'New...' tab. Name the
     340        experiment. Click 'Add raw bioassays...' button and mark the
     341        raw bioassays to add to the experiment and click
     342        'Ok'. Finalize with clicking the 'Save' button. </p>
     343      </li>
     345      </ol>
    292347    </ol>
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