The outputs of GISTIC

Question

[agicict]

Hi.

I am trying to find the meaning of GISTIC result files.

I cannot figure out how GISTIC does estimate real copy number of genes.

I read two papers about GISTIC but I could not find the algorithm for copy number estimation.

How does GISTIC make all_data_by_gene.txt file?

I also would like to know the meaning of minimum arm-level amplification level which is used for sample_cutoff.txt

Does minimum arm-level amplification mean a median of segemtns whose size are similar to the chromosome arm length?

[H.Hasani]

hi,

were you able to find the answer to your question?

Answer 1

[Kevin Blighe]

Please contact the GISTIC team directly:

• A: GISTIC input parameters.
• A: GISTIC 2.0 all threshold file versus genome browser

Kevin