Error when using TCGA CNA data to run ABSOLUTE
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Entering edit mode
9 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 • 323 views
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