Changeset 6958 for trunk/doc/test/roles/index.html

Timestamp:

Sep 30, 2015, 2:55:14 PM (8 years ago)

Author:

Nicklas Nordborg

Message:

References #1941: Store experimental factor values as part experiments

Updated test program to set experimental factor values on root raw bioassays instead of raw bioassays.

Noted that the "Item overview validation" now complains about missing experimental factors, probably because it has not been updated and still check the raw bioassays and not the root raw bioassays.

File:

• trunk/doc/test/roles/index.html (modified) (2 diffs)

trunk/doc/test/roles/index.html

@@ -2127 +2127 @@
   </li>
   
-  <li><a name="inheritannotations"></a>
-    Inherit the annotations from the scans, extracts, samples and biosource for each raw bioassay.
-    Use the <i>auto-inherit</i> function that exists on the experiment properties
-    tab. Make sure that all experimental factors are selected by the check boxes,
-    then click on the <i>Auto-inherit</i> link in the column header. <br>
-    <b>Note!</b> The <i>Dye swap</i>
-    annotation will not get values until the next step, and the <i>Affymetrix raw A.3</i>
-    data set is missing biomaterial parents with annotations.<br>
-    <b>Note 2!</b> In <i>Experiment A</i> there are duplicate values for the <i>RIN</i>
-    annotations. Fix this by manually removing the annotations that are inherited from
-    the <i>Extract A.ref.qc</i> extract. 
-    <p>
-
-  </li>
-  
   <li>
     Import raw data to the Genepix and Cufflinks raw bioassays. 
@@ -2242 +2227 @@
     
   </li>
+  
+  <li><a name="inheritannotations"></a>
+    Inherit the annotations from the scans, extracts, samples and biosource for each root raw bioassay.
+    Use the <i>auto-inherit</i> function that exists on the experiment properties
+    tab. Make sure that all experimental factors are selected by the check boxes,
+    then click on the <i>Auto-inherit</i> link in the column header. Use the <b>Inherit</b> 
+    option for some annotations and <b>Clone</b> option for some. Uncheck the <b>No duplicates</b>
+    option for the <i>RIN</i> annotation (see note 2 below).
+    <br>
+    <b>Note!</b> The <i>Affymetrix raw A.3</i>
+    data set is missing biomaterial parents with annotations.<br>
+    <b>Note 2!</b> In <i>Experiment A</i> there are duplicate values for the <i>RIN</i>
+    annotations. Verify and fix this by manually removing the annotations that are inherited 
+    from the <i>Extract A.ref.qc</i> extract (value=9.2). 
+    <p>
+
+  </li>
+  
   
   <li>