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<title>Contents (Cluster 3.0 for Windows, Mac OS X, Linux, Unix)</title>

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<span id="Contents"></span><div class="header">
<p>
Next: <a href="Introduction.html#Introduction" accesskey="n" rel="next">Introduction</a>, Previous: <a href="index.html#Top" accesskey="p" rel="prev">Top</a>, Up: <a href="index.html#Top" accesskey="u" rel="up">Top</a> &nbsp; [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
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<h4 class="node-heading">Contents</h4>
<span id="SEC_Contents"></span>
<h2 class="contents-heading">Table of Contents</h2>

<div class="contents">
<ul class="no-bullet">
<li><a id="toc-Introduction-1" href="Introduction.html#Introduction">1 Introduction</a></li>
<li><a id="toc-Loading_002c-filtering_002c-and-adjusting-data" href="Data.html#Data">2 Loading, filtering, and adjusting data</a>
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  <li><a id="toc-Loading-Data" href="Data.html#Loading-Data">2.1 Loading Data</a></li>
  <li><a id="toc-Filtering-Data" href="Data.html#Filtering-Data">2.2 Filtering Data</a></li>
  <li><a id="toc-Adjusting-Data" href="Data.html#Adjusting-Data">2.3 Adjusting Data</a>
  <ul class="no-bullet">
    <li><a id="toc-Log-transformation" href="Data.html#Log-transformation">2.3.1 Log transformation</a></li>
    <li><a id="toc-Mean_002fMedian-Centering" href="Data.html#Mean_002fMedian-Centering">2.3.2 Mean/Median Centering</a></li>
    <li><a id="toc-Normalization" href="Data.html#Normalization">2.3.3 Normalization</a></li>
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<li><a id="toc-Distance_002fSimilarity-measures" href="Distance.html#Distance">3 Distance/Similarity measures</a>
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  <li><a id="toc-Distance-measures-based-on-the-Pearson-correlation" href="Distance.html#Distance-measures-based-on-the-Pearson-correlation">3.1 Distance measures based on the Pearson correlation</a></li>
  <li><a id="toc-Non_002dparametric-distance-measures" href="Distance.html#Non_002dparametric-distance-measures">3.2 Non-parametric distance measures</a></li>
  <li><a id="toc-Distance-measures-related-to-the-Euclidean-distance" href="Distance.html#Distance-measures-related-to-the-Euclidean-distance">3.3 Distance measures related to the Euclidean distance</a>
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    <li><a id="toc-Euclidean-distance" href="Distance.html#Euclidean-distance">3.3.1 Euclidean distance</a></li>
    <li><a id="toc-City_002dblock-distance" href="Distance.html#City_002dblock-distance">3.3.2 City-block distance</a></li>
  </ul></li>
  <li><a id="toc-Missing-values" href="Distance.html#Missing-values">3.4 Missing values</a></li>
  <li><a id="toc-Calculating-the-distance-matrix" href="Distance.html#Calculating-the-distance-matrix">3.5 Calculating the distance matrix</a></li>
</ul></li>
<li><a id="toc-Clustering-techniques" href="Cluster.html#Cluster">4 Clustering techniques</a>
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  <li><a id="toc-Hierarchical-Clustering" href="Hierarchical.html#Hierarchical">4.1 Hierarchical Clustering</a>
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    <li><a id="toc-Centroid-Linkage-Clustering" href="Hierarchical.html#Centroid-Linkage-Clustering">4.1.1 Centroid Linkage Clustering</a></li>
    <li><a id="toc-Single-Linkage-Clustering" href="Hierarchical.html#Single-Linkage-Clustering">4.1.2 Single Linkage Clustering</a></li>
    <li><a id="toc-Complete-Linkage-Clustering" href="Hierarchical.html#Complete-Linkage-Clustering">4.1.3 Complete Linkage Clustering</a></li>
    <li><a id="toc-Average-Linkage-Clustering" href="Hierarchical.html#Average-Linkage-Clustering">4.1.4 Average Linkage Clustering</a></li>
    <li><a id="toc-Weighting" href="Hierarchical.html#Weighting">4.1.5 Weighting</a></li>
    <li><a id="toc-Ordering-of-Output-File" href="Hierarchical.html#Ordering-of-Output-File">4.1.6 Ordering of Output File</a></li>
    <li><a id="toc-Output-Files" href="Hierarchical.html#Output-Files">4.1.7 Output Files</a></li>
  </ul></li>
  <li><a id="toc-The-k_002dmeans-Clustering-Algorithm" href="KMeans.html#KMeans">4.2 The <em>k</em>-means Clustering Algorithm</a></li>
  <li><a id="toc-Self_002dOrganizing-Maps" href="SOM.html#SOM">4.3 Self-Organizing Maps</a></li>
  <li><a id="toc-Principal-Component-Analysis" href="PCA.html#PCA">4.4 Principal Component Analysis</a></li>
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<li><a id="toc-Running-Cluster-3_002e0-as-a-command-line-program" href="Command.html#Command">5 Running Cluster 3.0 as a command line program</a></li>
<li><a id="toc-TreeView-1" href="TreeView.html#TreeView">6 TreeView</a></li>
<li><a id="toc-Code-Development-Information" href="Development.html#Development">7 Code Development Information</a></li>
<li><a id="toc-Bibliography-1" href="Bibliography.html#Bibliography">8 Bibliography</a></li>

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