a problem with the result of GISTIC2.0

Question

[jamesrenwu]

I used GISTIC2.0 at GenePattern public server to deal with copy number profiles. But I got a problem about the result. In the "del_genes.conf_99.txt" file, there are two columes with the same cytoband "20p12.1". The q-values are the same, while the residual q-values for them are different. I don't know why there are two residual q-values for the same region. I hope someone can give me help.

20p12.1 1.72E-19(q-value) 1.72E-19 (residual q-value) chr20:14302876-15179819 (wide peak boundaries)
20p12.1 1.72E-19(q-value) 1 (residual q-value) chr20:1-63025520 (wide peak boundaries)

Answer 1

[ssv.bio]

Second one is totally incorrect (IMHO). Entire chromosome is called for. Chr 20 in human is 63mb in size.

[jamesrenwu]

I chose the value of "Broad Length Cutoff" as 0.7, how did this mistake in GISTIC2.0 happen. Do you know?