I am running GISTIC 2.0 in segmentation data from TCGA and I was wondering whether it is advisable to set the input parameters as default or change the different thresholds. Running the analysis with everything on default and by only changing the confidence level to 0.99, I got many regions amplified/deleted so I thought of making the significance criteria more strigent. What would be your advice? Is this kind of plot considered "normal" output?
Here is how a plot I get looks like for example.
Thank you in advance!
UPDATE: Followed some recommendations on the GISTIC forum, but still I get many amplified and deleted regions. Any help on how I could extract any meaningful results from such noisy plots?