Compute copy number log2ratio values from Affymetrix SNP arrays

From Array Suite Wiki

Jump to: navigation, search

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:

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.