Question: GISTIC 2.0 Segment CN
0
gravatar for gaiusjaugustus
3.3 years ago by
United States
gaiusjaugustus150 wrote:

I am currently formatting my data for use with the GISTIC 2.0.  In the documentation, it states that the Seg.CN column should be:

(log2() -1 of copy number)

 

I want to verify with someone who has used the software before that I should take the log of my copy numbers, and subtract one (1) to get this value.

Also, can anyone explain the significance of subtracting 1?

 

cnv gistic2.0 • 3.5k views
ADD COMMENTlink modified 3.0 years ago by rse90 • written 3.3 years ago by gaiusjaugustus150
5
gravatar for Eric T.
3.3 years ago by
Eric T.2.4k
San Francisco, CA
Eric T.2.4k wrote:

Yes, that's right. The values of this column are log2-scaled copy number relative to the normal copy number, which GISTIC assumes is 2 (diploid), so in this format the neutral regions will have a value 0.0, losses are negative numbers, and gains are positive.

Subtracting 1 after taking the log is the same as dividing by 2 before taking the log -- you're dividing the observed absolute copy number (e.g. 3) by the expected copy number (2): log2(3/2) = log2(3) - log2(2) = log2(3) - 1 = +0.58

(Why do they do this transformation? This format, SEG, was originally designed for array CGH and SNP arrays, where the measured values are log-scaled ratios like this, not absolute copy numbers.)

ADD COMMENTlink written 3.3 years ago by Eric T.2.4k
1
gravatar for rse
3.0 years ago by
rse90
Singapore
rse90 wrote:

Hi Etal,

What to do in case of absolute copy number 0?

Thanks

ADD COMMENTlink written 3.0 years ago by rse90
2

Try a number fairly close to zero, appropriate for the accuracy/precision of the measurement -- e.g. 0.001 in absolute scale is roughly -10 in log2 scale. GISTIC should handle these values OK.

ADD REPLYlink written 3.0 years ago by Eric T.2.4k

Thanks Etal. What about the number of markers?

ADD REPLYlink written 3.0 years ago by rse90
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