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
But from result download from http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/ABSOLUTE (data link is https://dm.genomespace.org/datamanager/file/Home/SpaceCadet/ABSOLUTE_demo/ABSOLUTE.review_results.zip the solid_tumor.segtab.txt file) is
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.
If anyone know how to reproduce result from http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/ABSOLUTE, please help me.
Thanks, Shixiang
