search help All Topics GeneChip® Arrays NetAffx™ Analysis Center Assays and Reagents Instruments Software

• System Requirements
• Installation
• File, Array and Sample Types Supported
• Backwards Compatibility
• QC for Genotyping
• Genotyping
• QC for Copy Number Analysis
• Copy Number Analysis
• Reference Sets
• Copy Number Polymorphism Analysis
• GTC Browser
• Heat Map Viewer

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Copy Number Analysis

Frequently Asked Questions

1. Which copy number workflows for the 100K Set/500K Array Set are supported in GTC 3.0.1?

2. Which copy number workflows for the SNP Array 6.0 are supported in GTC 3.0.1?

3. Which copy number analysis parameters are new or have changed in GTC 3.0.1?

4. What is the new Regional GC Correction algorithm enhancement for copy number analysis?

5. How is the Regional GC Correction algorithm enhancement implemented?

6. Why has the default value for the Confidence Score Threshold been changed to 1.0 in GTC 3.0.1?

7. Why has there been a parameter change in GTC 3.0.1 for gender calling in the copy number Segment Reporting Tool?

8. Can custom annotation files be used for copy number analysis in GTC 3.0.1?

9. Which CNV maps does the copy number Segment Reporting Tool use?

10. How are custom CNV maps used with the copy number Segment Reporting Tool?