Question: TCGA CNV Files Segment Mean
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gravatar for neenu.abraham8
4.5 years ago by
neenu.abraham850 wrote:

How can we calculate copy number variation(gain/loss/amplification/deletion)based on segment mean value or segment median  given in TCGA CNV file?Also suggest a  reference to such calculation

tcgi • 8.2k views
ADD COMMENTlink modified 8 months ago by Kevin Blighe41k • written 4.5 years ago by neenu.abraham850
2

A similar question and some answers How To Process The Cnv Level 3 Data From Tcga

In general a zero value corresponding to CN2. You have to define a threshold for a deletion and duplication. This group used -0.2 and 0.2, respectively. http://mcr.aacrjournals.org/content/12/4/485.long

 

 

 

ADD REPLYlink written 4.5 years ago by Jimbou680

Thanks for your information....

ADD REPLYlink written 4.5 years ago by neenu.abraham850
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gravatar for Kevin Blighe
8 months ago by
Kevin Blighe41k
The Ether
Kevin Blighe41k wrote:

I have given a full pipeline here, i.e., for taking the CN segment mean data and identifying recurrent gains and losses: C: How to extract the list of genes from TCGA CNV data

To then annotate the identified regions, take a look here: A: How to extract the list of genes from TCGA CNV data

Kevin

ADD COMMENTlink written 8 months ago by Kevin Blighe41k
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