Cannot reproduce ABSOLUTE example result
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Entering edit mode
4.1 years ago
Shixiang ▴ 100

I want to use ABSOLUTE, so I read documentation at http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/ABSOLUTE and run example data (solid_tumor) by GenePattern ABSOLUTE modules. However I cannot reproduce this result.

I set parameters following

The dataset samples are from a single human bladder cancer patient. The following parameters were used to obtain results: max sigma h = 0.2, min ploidy = 0.5, max ploidy = 8, primary disease = BLCA, platform = SNP_6.0, varied sample names, max non clonal = 1, and copy number type = total. For the two samples with somatic mutation data, min mut af = 0.1.

The question or interesting thing is, I got same result from ABSOLUTE module, but the final absolute copy number from ABSOLUTE.review ( the middle process is ABSOLUTE.summarize).

I just show few rows as following,

sample  Chromosome  Start.bp    End.bp  n_probes    length  seg_sigma   W   copy_ratio  modal_cn    expected_cn subclonal   cancer_cell_frac    ccf_ci95_low    ccf_ci95_high   hz
TCGA_AAA    1   3218610 14449771    5840    11231161    0.00164 0.00394 0.456   3   3.01608 0   1   1   1   0
TCGA_AAA    1   14450545    14453003    2   2458    0.08839 0   0.13051 1   1.40279 0   1   1   1   0
TCGA_AAA    1   14455748    31677633    9063    17221885    0.00131 0.00604 0.46211 3   3.05098 0   1   1   1   0
TCGA_AAA    1   31682380    31736123    40  53743   0.01976 2e-05   0.33972 2   2.37274 0   1   1   1   0
TCGA_AAA    1   31740706    31750640    4   9934    0.0625  0   0.56813 4   3.66599 0   1   1   1   0
TCGA_AAA    1   31751191    31829873    35  78682   0.02113 3e-05   0.69164 4   4.51108 0   1   1   1   0
TCGA_AAA    1   31832773    32252805    223 420032  0.00837 0.00015 0.80213 5   5.40756 0   1   1   1   0
TCGA_AAA    1   32253305    33264078    385 1010773 0.00637 0.00035 0.4496  3   2.97967 0   1   1   1   0
TCGA_AAA    1   33266475    70425743    22506   37159268    0.00083 0.01303 0.3384  2   2.36298 0   1   1   1   0


sample  Chromosome  Start.bp    End.bp  n_probes    length  seg_sigma   W   copy_ratio  modal_cn    expected_cn subclonal   cancer_cell_frac    ccf_ci95_low    ccf_ci95_high   hz
solid_tumor 1   3218610 14449771    5840    11231161    0.00164 0.00394 0.456   2   2.08205 0   1   1   1   0
solid_tumor 1   14450545    14453003    2   2458    0.08839 0   0.13051 0   0.58299 0   1   1   1   1
solid_tumor 1   14455748    31677633    9063    17221885    0.00131 0.00604 0.46211 2   2.11418 0   1   1   1   0
solid_tumor 1   31682380    31736123    40  53743   0.01976 2e-05   0.33972 1   1.47764 0   1   1   1   0
solid_tumor 1   31740706    31750640    4   9934    0.0625  0   0.56813 3   2.69295 0   1   1   1   0
solid_tumor 1   31751191    31829873    35  78682   0.02113 3e-05   0.69164 3   3.5209  0   1   1   1   0
solid_tumor 1   31832773    32252805    223 420032  0.00837 0.00015 0.80213 4   4.40417 0   1   1   1   0
solid_tumor 1   32253305    33264078    385 1010773 0.00637 0.00035 0.4496  2   2.04857 0   1   1   1   0


The modal_cn column is very different. However, both result have same purity 0.67 and ploidy 3.45.

array   sample  call status purity  ploidy  Genome doublings    delta   Coverage for 80% power  Cancer DNA fraction Subclonal genome fraction   tau E_CR
TCGA_AAA    TCGA_AAA    high entropy    0.67    3.45    0   0.22    18  0.78    0.01    3.34891105861831    0


I tried use ABSOLUTE R package and run example data many times, I all got same result.

I tried everything I can do but cannot reproduce the same absolute copy number result.

Thanks, Shixiang

absolute • 1.3k views
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Entering edit mode
3.5 years ago
plchen • 0

hi, Shixiang, I just use the absolute solfware for the first time, and I cannot understand how to produce the ABSOLUTE.review results show in the https://software.broadinstitute.org/cancer/cga/absolute_run, would you please provide the codes to get these results for me? thank you very much!