How does TCGA get Segment_Mean in files of copy number variations?

Question

[Ashleyca]

Hi all,

I have download the copy number variation file of Ovarian serous cystadenocarcinoma in TCGA.

How does TCGA get Segment_Mean (please see the following image) in the of copy number variations files? Is there any algorithm to calculate the Segment_Mean? What is the algorithm?

The file shown in the above image was downloaded in: https://gdc-portal.nci.nih.gov/search/s

The following image show the position where the file was downloaded:

Thanks for any help.

Answer 1

[Zhenyu Zhang]

These were calculated via CBS algorithm using tangent copy number data. The tangent data is derived from Birdsuite package from Affy SNP6 array.