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Genomics Suite Documentation

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  • Select Customize... to open the Advanced Import Options dialog
  • Choose No normalization in the Normalization section of the Algorithm tab
  • Select the Outputs tab (Figure 2)

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This spreadsheet contains copy number values per probe in log2 space (i.e. diploid = 0). This Prior to performing copy number analysis, you can normalize for local GC abundance.

  • Select Transform
  • Select Adjust Based on Local GC Content...
  • Click OK to run Local GC Adjustment (Figure 4)

Numbered figure captions
SubtitleTextAdjusting for local GC content
AnchorNameLocal GC Adjustment

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The GC adjusted spreadsheet is the starting spreadsheet for copy number analysis. You can now switch over to the Copy number workflow, skip the Create copy number step, and begin with the Detect amplifications and deletions step. Consult the user's guide for the copy number workflow for subsequent steps. 

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