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).