Duplicated expression values?
1
0
Entering edit mode
davi.vuko • 0
@01288822
Last seen 6 months ago
Austria

A rather large amount of entries contain a whole lot of genes with identical expression levels, especially some that should be vastly different, i.e. HLA-A and HLA-B.

Here's an example after fetching data using depmap_copyNumber(): depmap_id: ACH-000038 log_copy_number: 1.004462

which is found in 2550 different genes.

Here's another one:

example

I think I might be missing something here, could anyone help?

depmap_copyNumber() depmap • 506 views
ADD COMMENT
0
Entering edit mode

Do you know what copy number means? It's not a measure measure of gene expression

ADD REPLY
1
Entering edit mode
@laurent-gatto-5645
Last seen 2 days ago
Belgium

This was provided as an answer by email to OP. I copy it here so that other benefit from it:

We did not change any of these copy number values. Integer values in Depmap R package datasets are as-is. The genes with similar CNV counts are likely an artifact of normalization from their pipeline, which you can read more about here: https://depmap.sanger.ac.uk/documentation/datasets/copy-number/

If you have more specific questions about how this data was normalized, I suggest that you address your questions to depmap@sanger.ac.uk

ADD COMMENT
0
Entering edit mode

Thank you so much for the swift reply. I have contacted them and will update this thread as soon as I know more.

ADD REPLY
0
Entering edit mode

I'm learning about this value so I can find duplicate data more easily. Your shared link has effective real data for background knowledge https://depmap.sanger.ac.uk/documentation/datasets/copy-number/snake io

ADD REPLY

Login before adding your answer.

Traffic: 690 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6