Are 21Q4 CCLE_wes_gene_cn.csv copy number data log2-transformed

For version 21Q4, there are two more files: CCLE_wes_gene_cn.csv and CCLE_wes_segment_cn.csv. From the README file, the CCLE_wes_gene_cn.csv described the gene level copy number data and log2-transformed with a pseudo count of 1. Actually, these values were not transformed.

Test use following gene and cell line:

  • gene MYCN (4613), located in chr2:15,940,550-15,947,007
  • cell line ACH-000227

the value in CCLE_wes_gene_cn.csv is 196.31083614819093, same as the Segment_Mean value of segment chr2:15,941,812-15,946,349 in CCLE_wes_segment_cn.csv.

Thanks for reporting this. We will address this issue in an upcoming quarter.