Same values of copy number alteration (CNA) in 22Q1

Q&A
1

Dear Depmap community,
Greetings, I have a question about the CCLE_gene_cn.csv file in the 22Q1 version.
I saw that some copy number alteration (CNA) values in each cell line had identical values per gene.
As you can see in the below capture, is it possible that different genes have the same log2 fold-changed value in a cell line?
If not, can anyone check the file?

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image772×161 5.7 KB

Thanks,
Songyeon

2

Hello SongSong,

The way we compute gene level copy number is explained in our documentation I believe. it is just a weighted average of the segment CN values under that gene. in this case the genes are overlapping or in close proximity so it makes sense that they are almost always overlapping the same segments.

Hope this answers your question,

Best,

3

That can’t be correct. For each cell line, the cn value in the table is identical across all genes, which are arrayed as columns. Something is wrong here…

4

I take it back…I see it now. thanks for the info…

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