Users have asked us: What is relative copy number/copy number ratio?

Since we do not have matched normals, the output is a “copy ratio” or relative copy number. It is relative to the rest of the genome for that cell line. E.g. if the cell line is tetraploid we would not be able to see it from the relative copy number. These values are reported as log2(relative CN + 1…

Hi, Trying to understand in detail how to obtain relative copy number from absolute copy number values using the log2(relative CN + 1) formula: Example: A375 cell line, ploidy = 2.76 ENO4 gene, absolute CN = 3 Why is the relative copy number of ENO4 gene in A375 is 1.04 All values are taken fr…

The ‘relative CN’ is the Segment_Mean from the segment file that covers the gene (padded and averaged across the coordinates). For the cell line you’re pointing to (ACH-000219) ENO4 is covered by the following segment in the segment file: DepMap_ID Chromosome Start End Num_Probes Segment_Mean Sourc…

Hello, thank you for the explanations. To be clear - what is the equation relating relative copy number and absolute copy number? Is it absolute copy number = ploidy * (relative copy number) In which case in the example above , the discrepancy is between the report value for relative copy number …

Can anyone help with this question?

Hi, your interpretation seems correct to me. The ABSOLUTE results should be a better measure of ploidy, rather than using the equation that you have used here. So if you need to know the absolute copy numbers I would recommend using the results from ABSOLUTE. However, at the moment we do not update …

@jnoorbak , what does the Segment_Mean value represent when the Source is SNP array?

Hi, jnoorbak, You stated CN profile in DepMap is log2(relative CN + 1). However, in the source code of your copy number process pipeline pipeline , (key command: genecn = toGeneMatrix(gapmergedsegs, gene_mapping)), this toGeneMatrix function doesn’t take log operations (source code of this function…

Hi, the transformation happens here . We’re in the process of refactoring and cleaning up our code, so hopefully it will be more accessable for the users in the upcoming months.

What is relative copy number/copy number ratio?

Q&A

jnoorbak March 1, 2021, 11:12pm 9

The Segment_Mean for SNP array is based on a different pipeline. These are our legacy data which we have not reprocessed. The method can be found in SI2 (page 3) of the original CCLE paper.

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What is relative copy number/copy number ratio?

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