Cannot reproduce ABSOLUTE example result
1
1
Entering edit mode
3.0 years ago
Shixiang ▴ 80

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

absolute • 933 views
ADD COMMENT
0
Entering edit mode
2.4 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!

ADD COMMENT

Login before adding your answer.

Traffic: 2483 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6