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, dom, 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.