zRPKM normalization (Krumm et al., 2012) is available for CNV experiments and is calculated as follows:
zRPKM = (RPKM exon, sample – Median exon ) / StdDev exon
This is the optimal normalization method for CNV projects, as long as you have enough samples to provide a good standard deviation for each exon. Otherwise, we recommend using the RPKM-CN normalization method.
Note: When there are fewer than two experiments in the project, zRPKM normalization is disabled in the Set Up Preprocessing step and in Data Transformations.