C Extracting Affymetrix Copy Number Data for use in HelixTree

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 C.1 Extracting Affymetrix Copy Number Data Overview
 C.2 Creating CNT Files using the Affymetrix CNAT Batch Analysis Tool
  C.2.1 About Affymetrix CNAT
  C.2.2 Creating the CNT Files
 C.3 Creating CNCHP Files using Affymetrix Genotyping Console 2.0
  C.3.1 About Affymetrix Genotyping Console
  C.3.2 Generating CNCHP Files for the Mapping 100k and Mapping 500k Arrays
  C.3.3 Generating CNCHP Files for the Genome Wide SNP 6.0 Array
 C.4 Affymetrix CNT File Format
  C.4.1 Header Section
  C.4.2 Column Names Section
  C.4.3 Data Section
  C.4.4 Example File

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