To determine the copy number changes for a given transcript, we retrieved the segmented copy number scores of the tumor sample and the paired-normal control from the level 3 TCGA data, which were both inferred from the Affymetrix SNP 6.0 platform. Then for each transcript, we calculated the averages of the segmented copy number scores of the genetic interval between the transcription start and end sites as gene-based somatic copy number measure (Figure S4A, related to Figure 1).
