Hello,
After using GISTIC v2.0.23 in genepattern website, I found some unexpacted results. Some deletion peaks showed very significant q-values(4.43E-03~4.31E-08) but there is no significant actual copy number change across all samples. I checked actual copy number change for all samples in 'all_lesions.conf_95' file and the values were very low(-0.01~0.01), not even close to my cutoff value (t<-0.4). Could you please explain why I've got these results? Should I ignore these results?
I used champ.CNV group result as GISTIC input file. I set the following GISTIC parameters. Our GISTIC input sample size was 350 (bipolar patients). Deletion cutoff : -0.4 q-value cutoff : 0.0005 CI : 0.95 the other parameter was set as default.
Thank you for your advice. -Hyun
