How to use conumee segment mean for gistic input

Question

[Thind amarinder]

I have segment mean from methylation EPIC array ( when performing copy number analysis using conumee package) and want to use this with gistic tool which required "Seg.CN (log2() -1 of copy number)" column in the main input.

Someone explained here that "Segment means are the log2 ratio of the tumor intensity to the normal intensity. To convert to an absolute cn, use: (2^seg_mean)2".*

Not sure, if it's applicable to conumee o/p segment mean as well and copy number mentioned in the gistic documentation is absolute CN. Wondering if this column can be used directly since I will get the original values after two conversions (a) (2^seg_mean)*2" and (b) Seg.CN (log2() -1 of copy number).

[sativus]

Did you manage to find an answer to this question, i have done so myself, but would like to confirm that this methodology is sound?

[Thind amarinder]

Hi, I believe so, however, it is not confirmed by the author or anyone else from the tool development team. Please update, if you find some relevant information.