Compute copy number log2ratio values from Affymetrix SNP arrays

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Log2ratio in Affy SNP array is ratio between the sample and a reference sample set. We are using a training set (hapmap 270) as reference for log2ratio calculation, which is the same dataset used by other algorithms. Such as Affymetrix's powertool:

http://www.affymetrix.com/support/developer/powertools/changelog/apt-copynumber-workflow.html

There are two types of markers in Affy: one is associated with SNP ids; the other is simply copy number markers that are not SNPs.

http://www.affymetrix.com/browse/products.jsp?productId=131533#1_1