I am kind of sceptical about some results I got from GISTIC 2.0.
Using the following parameters I got a huge number of deleted genes while just a few amplified. More specifically, 587 amplified vs. 3461 deleted.
Input parameters used: Amplification Threshold = 0.1 Deletion Threshold = 0.1 Cap Values = 1.5 Broad Length Cutoff = 0.7 Remove X-Chromosome = 0 Confidence Level = 0.99 Join Segment Size = 4 Arm Level Peel Off = 1 Maximum Sample Segments = 2000 Gene GISTIC = 1
Are such results considered "normal"? Most of the publications I could find were not mentioning so many altered genes.
Thank you in advance. R.