Gistic2 warning: markers on largest gene exceed markers on smallest chromosome: overriding gene-gistic
0
0
Entering edit mode
3 months ago
tjbencomo ▴ 10

I'm running GISTIC2 on Sequenza generated segmentation data from whole exome tumor-normal pairs. I keep encountering the following warning:

Warning: markers on largest gene exceed markers on smallest chromosome: overriding gene-gistic
> In gene_score_permutations at 43
  In compute_stats at 83
  In run_focal_gistic at 201
  In run_gistic20 at 124
  In run_gistic2_from_seg at 249
  In gp_gistic2_from_seg at 97

I'm not really sure what this warning means and if I should be concerned about it affecting my results. According to the GISTIC documentation, the gene-gistic option "calculates the significance of deletions at a gene level instead of a marker level". What effect will this have on my results and should I be concerned?

Here is my GISTIC command:

./gistic2 -b $basedir \
    -seg $segfile \
    -refgene $refgenefile \
    -ta 0.1 \
    -armpeel 1 \
    -brlen 0.7 \
    -cap 1.5 \
    -conf 0.90 \
    -td 0.1 \
    -genegistic 1 \
    -gcm extreme \
    -js 4 \
    -maxseg 2000 \
    -qvt 0.25 \
    -rx 0 \
    -savegene 1 \
wes gistic2 cnv • 109 views
ADD COMMENT

Login before adding your answer.

Traffic: 2611 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6