for association between copy number of each CNA and the intensity of each probe. We included culture condition, gender and an interaction between copy number and culture condition as fixed effects; and used donor and assay batch as random effects. Q-values were obtained for each CNA using Benjamini Hochberg to adjust for multiple testing. The same approach was employed to test for association between X chromosome copy number and gene expression, but we limited the tests to female samples and to probes on the X chromosome.
