Entering edit mode
3.3 years 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