SNP6 PANCANCER data - which log()? broad.mit.edu_PANCAN_Genome_Wide_SNP_6_whitelisted.gene.xena

[Alex Azizi]

Dear Team,

Thank you again for the wonderful resource.

May I ask which log() the SNP6 data was converted with (log2 vs log10 vs ln)? I would like to set gain and amplification thresholds in my analysis so knowing what a doubling might represent in the datatable would be great.

Sincerely,
Alex

P.S.
dataset: copy number (gene-level) - tumor gene-level copy number (delete germline cnv, SNP6 array)hub: https://pancanatlas.xenahubs.net
cohortTCGA Pan-Cancer (PANCAN)
dataset IDbroad.mit.edu_PANCAN_Genome_Wide_SNP_6_whitelisted.gene.xena
downloadhttps://tcga-pancan-atlas-hub.s3.us-east-1.amazonaws.com/download/broad.mit.edu_PANCAN_Genome_Wide_SNP_6_whitelisted.gene.xena.gz; Full metadata
samples10873
version2016-12-29
type of datacopy number (gene-level)
unitlog(tumor/normal)

[Mary Goldman]

Hi Alex,

So glad we are useful to you! Looking at the paper where this data comes from (https://www.cell.com/cell/fulltext/S0092-8674(18)30302-7) the link to the copy number pipeline at the Broad Institute is unfortunately broken. Looking at the Circular Binary Segmentation algorithm that was used (https://pubmed.ncbi.nlm.nih.gov/15475419/) it looks as though the results it generates are log base 2. 

You can contact the GDC directly to confirm: https://gdc.cancer.gov/support as they are the official home of this data (https://gdc.cancer.gov/about-data/publications/pancanatlas). Sorry to not have a more definitive answer.

Best,

Mary

-----

Mary Goldman (she/her), Design and Outreach Engineer 

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

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[Alex Azizi]

Dear Mary,

Thank you for this detailed and illuminating response! It is really helpful. I will follow this up. 

Sincerely,

Alex