Is the default threshold of 0.1 for GISTIC2.0 good?
Hi everyone,
I work with human segmented data, and I am using GISTIC2.0. The default log2 threshold is 0.1. Above 0.1 = amplification, lower than 0.1 = deletion. I wanted to ask the community members what they think about this threshold since it is subjective, no?
Thank you
1 answer
In Jerby-Aron et al 2014 they used thresholds of -.3 and .3 for defining deletion/amplification. See the description in the Experimental Procedures:
Of note, the SCNA parameters (-0.3 and 0.3) used here are more stringent cutoffs compared to those used in the literature to define gene amplification and deletion (Beroukhim et al., 2010).
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You should note that it is not below 0.1 that is a deletion rather below -0.1.
Hi! Yes, sorry. In gene pattern, 0.1 is automatically converted to -0.1. :)