Ignore:
Timestamp:
Sep 30, 2015, 2:55:14 PM (6 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:
1 edited

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  • trunk/doc/test/roles/index.html

    r6124 r6958  
    21272127  </li>
    21282128 
    2129   <li><a name="inheritannotations"></a>
    2130     Inherit the annotations from the scans, extracts, samples and biosource for each raw bioassay.
    2131     Use the <i>auto-inherit</i> function that exists on the experiment properties
    2132     tab. Make sure that all experimental factors are selected by the check boxes,
    2133     then click on the <i>Auto-inherit</i> link in the column header. <br>
    2134     <b>Note!</b> The <i>Dye swap</i>
    2135     annotation will not get values until the next step, and the <i>Affymetrix raw A.3</i>
    2136     data set is missing biomaterial parents with annotations.<br>
    2137     <b>Note 2!</b> In <i>Experiment A</i> there are duplicate values for the <i>RIN</i>
    2138     annotations. Fix this by manually removing the annotations that are inherited from
    2139     the <i>Extract A.ref.qc</i> extract.
    2140     <p>
    2141 
    2142   </li>
    2143  
    21442129  <li>
    21452130    Import raw data to the Genepix and Cufflinks raw bioassays.
     
    22422227   
    22432228  </li>
     2229 
     2230  <li><a name="inheritannotations"></a>
     2231    Inherit the annotations from the scans, extracts, samples and biosource for each root raw bioassay.
     2232    Use the <i>auto-inherit</i> function that exists on the experiment properties
     2233    tab. Make sure that all experimental factors are selected by the check boxes,
     2234    then click on the <i>Auto-inherit</i> link in the column header. Use the <b>Inherit</b>
     2235    option for some annotations and <b>Clone</b> option for some. Uncheck the <b>No duplicates</b>
     2236    option for the <i>RIN</i> annotation (see note 2 below).
     2237    <br>
     2238    <b>Note!</b> The <i>Affymetrix raw A.3</i>
     2239    data set is missing biomaterial parents with annotations.<br>
     2240    <b>Note 2!</b> In <i>Experiment A</i> there are duplicate values for the <i>RIN</i>
     2241    annotations. Verify and fix this by manually removing the annotations that are inherited
     2242    from the <i>Extract A.ref.qc</i> extract (value=9.2).
     2243    <p>
     2244
     2245  </li>
     2246 
    22442247 
    22452248  <li>
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