https://wiki.biouml.org/index.php?action=history&feed=atom&title=Compute_differentially_expressed_genes_using_Limma_%28workflow%29 2026-04-21T23:28:19Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=Compute_differentially_expressed_genes_using_Limma_(workflow)&diff=7840&oldid=prev 2019-03-12T09:34:39Z

<p>Automatic synchronization with BioUML</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 09:34, 12 March 2019</td> </tr><tr><td colspan="2" class="diff-lineno">Line 5:</td> <td colspan="2" class="diff-lineno">Line 5:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Workflow overview ==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Workflow overview ==</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Compute-differentially-expressed-genes-using-Limma-workflow-overview.png|400px]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Compute-differentially-expressed-genes-using-Limma-workflow-overview.png|400px]]</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">== Description ==</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">This workflow is designed to identify differentially expressed genes from several experimental conditions applying Limma statistics. Normalized data can be generated from Affymetrix ([http://test.genexplain.com/bioumlweb/#de=analyses/Methods/Data normalization/Affymetrix normalization Affymetrix normalization]), Agilent ([http://test.genexplain.com/bioumlweb/#de=analyses/Methods/Data normalization/Agilent normalization Agilent normalization]) or Illumina ([http://test.genexplain.com/bioumlweb/#de=analyses/Methods/Data normalization/Illumina normalization Illumina normalization]) raw data and submitted as input. Also un-normalized count data derived from RNA-seq experiment can be used as input for this workflow. Please note that the ''Limma'' method requires two or more replicates for each condition. It is necessary to provide a unique name for each condition.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">The workflow compares up to five conditions / groups in one run. All possible comparisons between the input conditions are calculated in one workflow run. The first step of the workflow is a quality control of the input data and gives out a density boxplot and a density plot. The primary result of the Limma method is filtered by several conditions in parallel, applying the ''Filter table'' method to identify up- and down-regulated probeset IDs for each comparision.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Filteration criterion used is as follows:</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">'''Upregulated: logFC&gt;0.5 &amp;&amp; adj_P_Val &lt;0.05'''</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">'''Down regulated: logFC&lt;-0.5 &amp;&amp; adj_P_Val&lt;0.05'''</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">'''Non-changed genes logFC&lt;0.002 &amp;&amp; logFC&gt;-0.002'''</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">The output folder contains gene tables as well as the images of the density boxplots and density plots. </ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Reference: Smyth, G. K. (2005). Limma: linear models for microarray data. In: Bioinformatics and 68 RNA-seq Computational Biology Solutions using R and Bioconductor. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds), Springer, New York, 2005.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Parameters ==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Parameters ==</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Input table</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Input table</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:Input table with all normalized <del class="diffchange diffchange-inline">CEL </del>files</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:Input table with all normalized files</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Probe type</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Probe type</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Species</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Species</div></td></tr> </table>

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<p>Automatic synchronization with BioUML</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 12:02, 13 February 2017</td> </tr><tr><td colspan="2" class="diff-lineno">Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Probe type</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Probe type</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Species</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Species</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>;<del class="diffchange diffchange-inline">Condition </del>1</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>;<ins class="diffchange diffchange-inline">Condition_1</ins></div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>;<del class="diffchange diffchange-inline">Condition </del>2</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">:Please enter condition or group name </ins>1</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>;<del class="diffchange diffchange-inline">Condition </del>3</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>;<ins class="diffchange diffchange-inline">1_Columns</ins></div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>;<del class="diffchange diffchange-inline">Condition </del>4</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">:Select columns for condition 1</ins></div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>;<del class="diffchange diffchange-inline">Condition </del>5</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">;Condition_2</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">:Please enter condition or group name </ins>2</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>;<ins class="diffchange diffchange-inline">2_Columns</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">:Select columns for condition 2</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">;Condition_3</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">:Please enter condition or group name </ins>3</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>;<ins class="diffchange diffchange-inline">3_Columns</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">;Condition_4</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">:Please enter condition or group name </ins>4</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>;<ins class="diffchange diffchange-inline">4_Columns</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">;Condition_5</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">:Please enter condition or group name </ins>5</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">;5_Columns</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Results folder</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Results folder</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> </table>

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<p>Protected &quot;<a href="/index.php/Compute_differentially_expressed_genes_using_Limma_(workflow)" title="Compute differentially expressed genes using Limma (workflow)">Compute differentially expressed genes using Limma (workflow)</a>&quot;: Autogenerated page (‎[edit=sysop] (indefinite))</p> <table class='diff diff-contentalign-left'> <tr style='vertical-align: top;'> <td colspan='1' style="background-color: white; color:black;">← Older revision</td> <td colspan='1' style="background-color: white; color:black;">Revision as of 05:21, 25 August 2015</td> </tr></table>

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<p>Automatic synchronization with BioUML</p> <p><b>New page</b></p><div>;Workflow title<br /> :Compute differentially expressed genes using Limma<br /> ;Provider<br /> :[[geneXplain GmbH]]<br /> == Workflow overview ==<br /> [[File:Compute-differentially-expressed-genes-using-Limma-workflow-overview.png|400px]]<br /> == Parameters ==<br /> ;Input table<br /> :Input table with all normalized CEL files<br /> ;Probe type<br /> ;Species<br /> ;Condition 1<br /> ;Condition 2<br /> ;Condition 3<br /> ;Condition 4<br /> ;Condition 5<br /> ;Results folder<br /> <br /> [[Category:Workflows]]<br /> [[Category:GeneXplain workflows]]<br /> [[Category:Autogenerated pages]]</div>

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