Error when using TCGA CNA data to run ABSOLUTE
0
0
Entering edit mode
19 months ago
Mark • 0

Hello everybody,

I am trying to analyse CNV data from TCGA to get a measure of overall CNV per patient. Therefore, I downloaded the Level 3 files taken from the SNP6 array from FireBrowse, and I ran ABSOLUTE in R.

RunAbsolute(seg.dat.fn = "dir/ESCA.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg18__seg.seg.txt",
min.ploidy = 1, max.ploidy = 50,
max.sigma.h = 6,
platform = "SNP_6.0",
copy_num_type = "total",
sigma.p = 0,
results.dir = output.dir,
primary.disease="EAC",
sample.name = "Sample",
max.as.seg.count = 15000,
verbose = T)


The ABSOLUTE function runs, but while running it returns an error:

Error in seq.default(dom[1], dom[2], d_res) :
'from' must be a finite number
In addition: There were 50 or more warnings (use warnings() to see the first 50)
enter code here


Does anyone know what triggered this error? I am afraid that it is a simple mistake, but it already took quite a lot of time to find a fix. I hope that the collective knowledge of Biostars can help me out.

Best, Mark

tcga copynumber absolute • 454 views
ADD COMMENT

Login before adding your answer.

Traffic: 558 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