25 Copy Number Analysis (Optional Module)

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 25.1 Copy Number Analysis Overview
  25.1.1 Copy Number Variation
  25.1.2 The Copy Number Analysis Module (CNAM)
 25.2 Preparing the Log2 Ratio Data
 25.3 Using the Copy Number Analysis Segmentation Tool
  25.3.1 The DSF File
  25.3.2 Chromosome Selector
  25.3.3 Segmenting Options
  25.3.4 Optional File Output
  25.3.5 Exclude Markers
  25.3.6 Run Log
 25.4 Outputs of the Copy Number Analysis Segmentation Tool
  25.4.1 Log2Ratio Covariates Dataset
  25.4.2 Log2Ratio Segments Dataset
  25.4.3 Wiggle Track (WIG) File
 25.5 Import LogR DSF Values Directly
 25.6 Save LogR DSF Values as CNT Files
 25.7 Using the LogR Association Tests and PCA Window
  25.7.1 Introduction
  25.7.2 Data Requirements
  25.7.3 Available Tabs
  25.7.4 Input Tab
  25.7.5 Description of Association Testing
  25.7.6 PCA Correction
  25.7.7 Principal Component Analysis Parameters Tab
  25.7.8 Exclude SNPs Tab
 25.8 Visualizing Copy Number Analysis Results
  25.8.1 BeadStudio Genome Viewer
  25.8.2 UCSC Genome Browser
  25.8.3 Affymetrix IGB
 25.9 Copy Number Analysis Examples and Tutorials
  25.9.1 Univariate Segmenting Example
  25.9.2 Multivariate Segmenting Example
  25.9.3 Data Quality Tutorial
 25.10 Golden Helix Copy Number Segmentation Algorithm
  25.10.1 Overview
  25.10.2 Obtaining Segments with a Moving Window
  25.10.3 Obtaining Segments without a Moving Window
  25.10.4 Copy Number Segmentation within a Sub-Region
  25.10.5 Permutation Testing for Verifying Copy Number Segments
 25.11 Workflow for Reading Affymetrix CEL Files

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