https://sourceforge.net/p/altanalyze/wiki/MarkerFinder/Recent changes to MarkerFinderenSat, 01 Feb 2014 01:06:20 -0000https://sourceforge.net/p/altanalyze/wiki/MarkerFinder/<div class="markdown_content"><h2 id="marker-discovery-analysis-in-altanalyze">Marker Discovery Analysis in <a class="" href="../AltAnalyze">AltAnalyze</a></h2> <p><a class="" href="../AltAnalyze">AltAnalyze</a> includes a built-in method to identify putative markers that are selectively expressed in a single analyzed condition. This method is most appropriate when analyzing greater than 2 biological groups to discover genes or other IDs that can optimally distinguish a given biological group from all others. <a class="" href="/p/altanalyze/wiki/MarkerFinder/">MarkerFinder</a> is run by default in the standard <a class="" href="../AltAnalyze">AltAnalyze</a> workflows. </p> <p>This approach is distinct from the <a class="" href="/p/altanalyze/wiki/SampleClassification/">LineageProfilerIterate</a> approach, which allows for more sophisticated marker identification, along with training and evaluation methods (see <a class="" href="/p/altanalyze/wiki/SampleClassification/">SampleClassification</a>). </p> <h3 id="core-algorithm">Core Algorithm</h3> <p>The core algorithm is the same one used for the <a class="" href="../LineageProfiler">LineageProfiler</a> cell-type marker discovery pipeline as described <a class="" href="http://code.google.com/p/altanalyze/wiki/LineageProfiler#Building_the_Lineage_Marker_Databases" rel="nofollow">here</a>. </p> <h3 id="default-analysis">Default Analysis</h3> <p>By default, <a class="" href="/p/altanalyze/wiki/MarkerFinder/">MarkerFinder</a> is run when performing a standard <a class="" href="../AltAnalyze">AltAnalyze</a> expression Analysis. Both tabular and heatmap image files will be produced. The tabular files are saved to the folder <a class="" href="../ExpressionOutput">ExpressionOutput</a>/<a class="" href="/p/altanalyze/wiki/MarkerFinder/">MarkerFinder</a> and the heatmap image files are saved to DataPlots/<a class="" href="/p/altanalyze/wiki/MarkerFinder/">MarkerFinder</a>. </p> <h3 id="application-of-markerfinder-results-for-sample-classification">Application of <a class="" href="/p/altanalyze/wiki/MarkerFinder/">MarkerFinder</a> Results for Sample Classification</h3> <p><a class="" href="/p/altanalyze/wiki/MarkerFinder/">MarkerFinder</a> result files can be loaded as input in the <a class="" href="../LineageProfiler">LineageProfiler</a> analysis menu. First, download <a class="" href="../AltAnalyze">AltAnalyze</a> from <a href="http://www.altanalyze.org" rel="nofollow">http://www.altanalyze.org</a>, extract to your hard drive and install the latest human database when prompted (currently EnsMart65) after running the first time. From the Main Menu select “vendor/data type” as “Other ID” and under “platform” select “Symbol”, then select “Continue”. Next, select “Additional Analyses” then select “Continue”. Next, select the menu item “Lineage Analysis” and “Continue”. </p> <p><img alt="" src="http://altanalyze.org/image/LineageProfilerScreen.png" rel="nofollow" /></p> <p>You will be presented with the analysis window to upload you expression (e.g., delta CT) values for your analyzed set of IDs (e.g., genes) and a reference expression file containing your two classes (e.g., cancer and wt) (“Select an alternative <a class="" href="/p/altanalyze/wiki/MarkerFinder/">MarkerFinder</a> reference file”). Next, you can optionally select the option “Select marker models to restrict analysis to”, to select a file with different ID sets to analyze. Leave the other options as default and select continue to run. </p> <p>Additional details can be found <a class="" href="/p/altanalyze/wiki/SampleClassification/">here</a>. </p></div>AnonymousSat, 01 Feb 2014 01:06:20 -0000https://sourceforge.net1fc8da2b855ace1c3f0db86a531fa75fbbb9b7c2