Normalize copy number data using autosomes Check this option to perform a two-step normalization on copy number intensity data: • First, the observations from non-autosomes (X and Y) are separated from autosomes . • The normalization is then applied only to autosome data. • For each observation from non-autosomes, normalized data from the nearest smaller and nearest larger autosomes are interpolated. Note : Checking this box disables the parameters corresponding to Baseline Reference for quantile normalization. To Normalize Copy Number Data Using Non-autosomes: Check the box.