1. How do I obtain GISTIC?
GISTIC is available either through the GenePattern server, at:
or as a standalone executable, at
The GISTIC module takes segmented copy-number data and generates plots of significance levels for amplifications and deletions, lists of regions that pass a preset significance threshold, tables indicating which samples are amplified or deleted in these regions, and lists of genes within each region.
A GISTIC_Preprocessing module, which prepares microarray data for segmentation analysis, is also available at these locations, but has not undergone complete testing.
2. Can you show me how to run GISTIC on GenePattern?
We have set up a pipeline, called Beroukhim.Getz.2007.PNAS.Glioma.GISTIC, that collects the example datasets and runs them through GISTIC. All you need to do is click “Run”. If you click “Properties” and then click on the arrow next to “GISTIC”, you can see the parameters used.
3. I get the following error:
??? Index exceeds matrix dimensions.
Error in ==> make_D_from_seg at 180
Error in ==> run_gistic_from_seg at 58
Error in ==> gp_gistic_from_seg at 179
It is possible that you're using the wrong markers file. You'll get that error if you use our example markersfile, rather than one designed to fit your data. If you used the GenePattern version of GLAD to segment your data, a reasonable markers file would be the first 3 columns of the input to GLAD.