Hi Biostars!
I am currently undertaking a CNA-analysis, in which i have access to methylation array data (Infinium EPIC). After generating CNV data through conumee, i would like to use this output for further processing using Gistic 2 to study CNAs at a gene level. The documentation of gistic states that in the input file for the Seg.CN column, it requires (log2() -1 of copy number) for each segment. This to my understanding is the same value as the "segment_mean" column in the conumee output (as it represents the log2 ratio of the intensity of group X compared to the intensity of group Y).
My question is thus, am i correct in making the assumption that the values found in the segment_mean column in the conumee output, can be used directly as values for the Seg.CN column as input for Gistic 2?
