0.5 limit-of-detection
giuili2025-cibersort-wgbs-tt limit-of-detection (median at 62M aligned reads)
- Tested configuration
- CIBERSORT (DecoNFlow benchmark)
- Protocol
- DecoNFlow WGBS-TT tumour-fraction limit of detection
- Dataset
- DecoNFlow benchmark WGBS-TT in silico mixtures
- Procedure
- ctdnameth-20261009-protocol-giuili2025-wgbs-tt-tumour-fraction-lod
- Evaluation
- CIBERSORT tumour-fraction LoD (WGBS-TT)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Independent external evaluation · source checkedA benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, G12; row 'CIBERSORT'; column '62M' under 'WGBS-TT'
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
Reproduction
- Split
- Four depths (62M, 183M, 310M, 620M aligned reads), ten tumour fractions from 0.01% to 50% plus 0%, ten replicates each
- Adaptation
- Not reported
- Scoring implementation
- Lowest tumour fraction at which the estimated fractions of the ten replicates are significantly higher than those of 0% tumour samples (one-tailed unpaired Mann-Whitney U test, Benjamini-Hochberg adjusted p < 0.01), moving from higher to lower fractions
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 0.5000 Individual claims | A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow Supplementary Table 3 sheet A, G12; row 'CIBERSORT'; column '62M' under 'WGBS-TT' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2025-11-27; not peer reviewed | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 independent paper Audit detailsExtracted by deterministic parse of the pinned XLSX cell XML (extract/rawxlsx.py, extract/extract_ctdna_methylation.py) with row and column labels asserted. printed_value is the shortest round-trip decimal of the stored cell value, or the displayed text where the workbook applies a fixed-decimals number format (recorded in workbook_number_format); raw_xml_value keeps the stored text. Independent review 2026-10-09: value and identity match the source. Field: Source artifact SHA-256: Hash scope: Not reproducible by re-download: bioRxiv rewrites the PDF on each download (ModDate and XMP dates set to the download time). A copy retrieved 2026-10-09T20:21:09Z has the same length (7,728,127 bytes) and SHA-256 fa7bcf8c25532f86dc99ed7d76a13a49ae70e29ab9f46559b3e0972e86aa9b96; resetting its three date stamps to any time on that day does not give the pinned hash, so another per-download field also differs. No result value is taken from this PDF. Extraction artifact SHA-256: |
| Reported result 0.5000 Individual claims | Giuili et al. 2025, Supplementary Table 3 (median limit of detection) Supplementary Table 3 sheet A, G12; row 'CIBERSORT'; column '62M' under 'WGBS-TT' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv version 1 supplementary file media-5.xlsx | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 independent paper Audit detailsExtracted by deterministic parse of the pinned XLSX cell XML (extract/rawxlsx.py, extract/extract_ctdna_methylation.py) with row and column labels asserted. printed_value is the shortest round-trip decimal of the stored cell value, or the displayed text where the workbook applies a fixed-decimals number format (recorded in workbook_number_format); raw_xml_value keeps the stored text. Independent review 2026-10-09: value and identity match the source. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
Sources and history
Release 2026-10-09-8cc1db47c7f9 · Record review: source checked
2 source records and release history
- A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow · Original source · bioRxiv preprint version 1, posted 2025-11-27; not peer reviewed
- Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Original source · bioRxiv version 1 supplementary file media-5.xlsx
Technical metadata and extraction receipts
Stable ID: ctdnameth-20261009-result-giuili2025-cibersort-wgbs-tt-62m-lod
- metric
- limit-of-detection
- metric qualifier
- median at 62M aligned reads
- metric direction
- lower
- unit
- fraction
- printed value
- 0.5000
- numeric value
- 0.5
- source locator
- Supplementary Table 3 sheet A, G12; row 'CIBERSORT'; column '62M' under 'WGBS-TT'
- raw xml value
- 0.5
- review
- method: source-hash-verification; deterministic-table-parse; independent-cell-check; method note: Re-downloaded the workbook and matched its SHA-256. Read the cell with a separate stdlib OOXML reader written for this review (shared strings, raw cell text and number format from styles.xml); the extractor's scripts were not imported or run. Checked raw text, printed value (fixed-decimals display where the cell format applies one, otherwise shortest round-trip decimal), numeric value, metric, qualifier, unit, direction, denominator or scored n, and the linked evaluation's configuration and protocol against the row and column headers. Every sheet A value was also compared with preprint Figure 4A (text layer).; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-09; artifact sha256: c585f11e0b128705d8c224fc8551b3f1c2efe52fa568c0e0dc96e37abaaced32; retrieval url: https://www.biorxiv.org/content/biorxiv/early/2025/11/27/2025.11.27.688590/DC5/embed/media-5.xlsx; note: Extracted by deterministic parse of the pinned XLSX cell XML (extract/rawxlsx.py, extract/extract_ctdna_methylation.py) with row and column labels asserted. printed_value is the shortest round-trip decimal of the stored cell value, or the displayed text where the workbook applies a fixed-decimals number format (recorded in workbook_number_format); raw_xml_value keeps the stored text. Independent review 2026-10-09: value and identity match the source.
- missing metadata
- uncertainty: reason: unreported
- unit detail
- Tumour DNA fraction of the mixture
- workbook number format
- 0.0000
Related records
- evaluation: CIBERSORT tumour-fraction LoD (WGBS-TT)