<p>From the library table it is also possible to launch a digital differential display analysis. First
select DDD in the bottom left menu (1). This will limit the layout of the left columns of the table to two
pools.<br/>
(2) Select the significant threshold for setting the type one error rate (0.05 correspond to a risk of 5% for the p-value corrected by FDR)
<br/>
Then select the libraries to be merged in the pools.<br/></p>
<img src="js/view/help/img/ddd_launch.jpg"/>
<p>Then click on the run button.</p>
<h2 class="help">Processing</h2>
<p>
The following frame will appear.
This frame shows the selected library pools with the corresponding colours and invite you to
enter your e-mail address because of the time needed to process the data.</p>
<img src="js/view/help/img/ddd_enter_email.jpg"/>
<p>
Once the processing is finished an e-mail will be sent to your address. This e-mail contains a
link to the DDD results.</p>
<img src="js/view/help/img/ddd_email.jpg"/>
<h2 class="help">Results</h2>
<p>
Clicking on the link will redirect you to the corresponding web page (example shown on the
next page).
</p>
<img src="js/view/help/img/ddd_result.jpg"/>
<p>
The result page contains four parts :
</p>
<ol class="help">
<li>The top page block presents the informations about the chosen library pools, the selected
significance threshold and the general figures about the number of contigs over-expressed
contigs in either pools or expressed in only one of the pools. It also includes the links to
download the complete results set containing eight files out of which three can be used to
query GO terms at the Wego website : http://wego.genomics.org.cn .
<ol class="help">
<li> expressed_only_in_pool2.wego</li>
<li> expressed_only_in_pool1.wego</li>
<li> expressed_only_in_pool2.tsv</li>
<li> overexpressed_only_in_pool1.wego</li>
<li> overexpressed_only_in_pool2.wego</li>
<li> expressed_only_in_pool1.tsv</li>
<li> overexpressed_only_in_pool1.tsv</li>
<li> overexpressed_only_in_pool2.tsv</li>
</ol>
</li>
<li> The second block presents 20 contigs over-expressed in pool 1 or in pool 2, the line of the overexpressed element is colored with the color in wich pool it's overexpressed</li>
<li> The third block presents 20 contigs only expressed in pool 1.</li>
<li> The fourth block presents 20 contigs only expressed in pool 2.</li>
</ol>
<h2 class="help">Wego Gene Ontology analysis</h2>
To perform a wego differential analysis, first uncompress the all_data.zip file, then go the
wego website (http://wego.genomics.org.cn) and load the files using the wego native format.
