ABSOLUTE using Oncoscan copy number


I am trying to run ABSOLUTE using Oncoscan data. It works for some samples, for others the expected copy number ratio is too high:

[1] "Capping 0 segs at tCR = 5.0"
[1] "Expected copy-ratio = 1.37009"

It would seem that in those cases the mean segment values are centered around 1, instead of 0. Probably because the ploidy is 3 instead of 2. If I center the segment values around zero by subtracting the mean of the segment values there is no problem.

Is one supposed to center the mean segment values around 0 when using Oncoscan data?

Should I run ABSOLUTE specifying the platform to be SNP_6.0?

Do you recommend against using Oncoscan data for Absolute?


ABSOLUE ; Capping 0 segs at tCR = 5.0

Hi ,

I met the same problem.

[1] "Capping 0 segs at tCR = 5.0"
[1] "Expected copy-ratio = 1.28202"
[1] "Mode flag is NA, not generating plots. Sample has failed ABSOLUTE"
[1] TRUE

But I am sure that I used human samples.

The segment file I used were computed by Varscan2 by comparing tumor and normal samples with exome sequence. Then it be used as input of ABSOLUE.

So, did I use the corrected pipeline?

I already set the max.as.seg.count to a really max value 1500000, still not work.
How to solve this problem?

Thank you