I’ve downloaded a dataset with gene relative copy numbers. As suggested in (https://forum.depmap.org/t/what-is-relative-copy-number-copy-number-ratio/), I calculated absolute copy numbers from relative copy numbers using the formula:
Absolute CN = Line ploidy * relative CN = Line ploidy * ((2 ** relative CN from the dataset) - 1)
I then rounded the results and compared some of them to the data from Absolute Copy Number section in the data explorer. While most of my results (est. 90%) agreed with the data explorer, other results were off. For example:
SKBR3 line, ploidy = 4.04 (Ploidy data from CCLE_ABSOLUTE_combined_20181227):
Gene EFCAB5, RCN = 1.626; ACN = 4.04 * ((2 ** 1.626) - 1) = 4.04 * 2.095 = 8.426 (Data Explorer, ACN = 7)
Gene NLRP3, RCN = 0.872; ACN = 4.04 * ((2 ** 0.872) - 1) = 4.04 * 0.830 = 3.356 (Data Explorer, ACN = 4)
SKMEL28 line, ploidy = 4.02
Gene C1orf194, RCN = 1.484; ACN = 4.02 * ((2 ** 1.484) - 1) = 4.02 * 1.797 = 7.225 (Data Explorer, ACN = 6)
Am I using an inaccurate formula? How is the ACN calculated? I haven’t found a relevant dataset or discussion about it.
Thanks in advance!