Changeset 2810

Timestamp:

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

Author:

Jari Häkkinen

Message:

Improving getting started doc.

File:

• trunk/doc/user/getting_started.html (modified) (2 diffs)

trunk/doc/user/getting_started.html

@@ -275 +275 @@
             box. Finalize with 'Save'. For Affymetrix the import is
             done, whereas Genepix have to perform reporter map
-            import. </p>
+            import. Remember to share your designs (normally to group
+            'Everyone'). </p>
 
             <p> <i>Genepix reporter map import</i> <br> Click on the
@@ -290 +291 @@
       </li>
 
+      <p> A normal user is not allowed to add array design, reporter
+      information, and a lot of other information to BASE. The reason
+      for this is that a lot of information should only exist as one
+      copy in the database. For example, reporters should only exist in
+      one copy because everyone uses the same reporters. There is no
+      need to store several copies of the same array design. </p>
+
+      <p> A user will normally upload experimental data to BASE for
+      import into the database. To be able to import the data, the
+      array design used must be available in BASE at import time. If
+      the array design is not available, a user with the proper
+      credential must add the array design to BASE. </p>
+
+      <ol type=a>
+
+      <li>
+        <p> <b> Create a new Project </b> <br> Go to 'View' ->
+        'Projects' and click on the 'New...' tab. Name the project and
+        save. In the projects listing page, click 'Set active' for the
+        new project. The selected project should be displayed on top
+        right as 'Active project'. Selecting an active project will
+        influence the behaviour of BASE. Only information related to
+        the active project will be displayed and items created will
+        automatically be shared to the active project. </p>
+
+        <p> The display of items shared to the active project only
+        requires that the 'view/presets' pull-down menu options are
+        properly set. In 'view/preset' you can select what should be
+        displayed, and if only 'In current project' is selected then
+        only information shared to a project will be shown. </p>
+      </li>
+
+      <li>
+        <p> <b>Create raw bioassays</b> <br> Upload your raw data
+        files. Go to 'View' -> 'Raw bioassays' and click on the
+        'New...' tab. Name the raw bioassay. Select 'Raw data
+        type'. Select the 'Array design', if you cannot see see
+        designs in the pop-up the make sure that the 'view/presets'
+        pull-down menu has 'Shared to me' marked and select appropriate
+        design. Select 'CEL file' if you create an Affymetrix raw
+        bioassay. You can leave the rest untouched. Redo for all raw
+        data files. (Yes a batch creator would be nice.) </p>
+      <li>
+
+      <li>
+        <p> <b>Create a new experiment</b> <br> Go to 'View' ->
+        'Experiments' and click on the 'New...' tab. Name the
+        experiment. Click 'Add raw bioassays...' button and mark the
+        raw bioassays to add to the experiment and click
+        'Ok'. Finalize with clicking the 'Save' button. </p>
+      </li>
+
+      </ol>
+
     </ol>