Should I run GISTIC2.0 for cases/controls separately?
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8 weeks ago
@e95917ed • 0

I am trying to analyze the differences in copy number alterations (CNA) between two classes of samples: cases and controls. Since GISTIC2.0 takes a group of samples and find focal CNAs, is it better to run GISTIC2.0 separately on my cases and controls, or should I run it on all samples combined?

My concern is that if i run GISTIC2.0 on all samples combined, some regions that are amplified/deleted only in the cases (or vice versa) might not show up in the results since GISTIC2.0 will only see amplifications/deletions in a smaller subset of the samples.

Any insight is appreciated! Thank you in advance.

GISTIC2.0 CNV CNA • 194 views
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tbh I never used GISTIC in a case-control manner, IMO it is designed for case-only use-case

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Thank you for your response! Do you have other tools that you recommend I use for case-control manner to analyze differences in CNAs?

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