Dear all,

I'm new to CNV analysis and am trying to analyze CNV between 5 cancer cells and 5 normal cells. The data is from Affymetrix SNP6.0. I used Affymetrix power tools(apt-copynumber-workflow).

For input option: --reference-input, the quick start section in the manual (http://media.affymetrix.com/support/developer/powertools/changelog/apt-copynumber-workflow.html) uses A reference file built using 270 Affymetrix Hapmap samples run at Affymetrix. Is it correct that if my goal is to compare disease and normal samples, I need to build my own reference by first running only the normal samples and use the output from --reference-output as a new reference and run only the cancel samples for the second run?

Regarding output - what do the following output columns mean? I cannot find any manual that explains this:

• Log2Ratio : What is this ratio?
• SmoothSignal
• LOH
• Allele differences

Any direction on where I can find these answers is appreciated. Thanks a lot in advance!