27.1 regression-intercept
carbo2022-family-cutoff-0-kraken2-excl-human-norm regression-intercept (linear regression between assigned read count and PCR Ct value)
- Tested configuration
- Kraken2, human reads removed, and assigned read counts normalised by target genome length (Carbo et al. 2022)
- Protocol
- Respiratory virus detection against PCR, family level, read-count cut-off 0 (Carbo et al. 2022 Supplementary Table 1)
- Dataset
- Nasal washings from COPD patients with respiratory complaints, metagenomic sequencing and 13-target respiratory PCR panel (Carbo et al. 2022)
- Procedure
- rna-pathogen-20261009-protocol-carbo2022-family-cutoff-0
- Evaluation
- Kraken2, human reads removed, and assigned read counts normalised by target genome length: family level, read-count cut-off 0 (Carbo et al. 2022)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Independent external evaluation · source checkedCarbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Family', block 'excl. human reads and normalized', cell J30, row 'Kraken2', column 'LR intercept'
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
- Whole cohort
- Adaptation
- Viral RefSeq database built 2020-12-27 (Genome Detective: own database)
- Scoring implementation
- Authors' ROC analysis over read-count cut-offs
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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 27.1 Individual claims | Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 Supplementary Table 1 sheet 'Suppl table 1-Family', block 'excl. human reads and normalized', cell J30, row 'Kraken2', column 'LR intercept' Version: medRxiv 2022.01.21.22269647 version 1 (2022-01-21), supplementary file media-1.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/extract_rna_pathogen.py), with row and column labels asserted. printed_value is the cell text, or the shortest decimal that round-trips to the stored number; displayed spreadsheet formatting was not applied. Pending independent review. 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
- Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Original source · medRxiv 2022.01.21.22269647 version 1 (2022-01-21), supplementary file media-1.xlsx
- Performance of Five Metagenomic Classifiers for Virus Pathogen Detection Using Respiratory Samples from a Clinical Cohort · Original source · Pathogens 11(3):340, published 2022-03-11; PMC8953373 full-text XML
Technical metadata and extraction receipts
Stable ID: rna-pathogen-20261009-result-carbo2022-family-cutoff-0-kraken2-excl-human-norm-lr-intercept
- metric
- regression-intercept
- metric direction
- unknown
- unit
- unitless
- printed value
- 27.1
- numeric value
- 27.1
- source locator
- Supplementary Table 1 sheet 'Suppl table 1-Family', block 'excl. human reads and normalized', cell J30, row 'Kraken2', column 'LR intercept'
- missing metadata
- uncertainty: reason: unreported
- metric qualifier
- linear regression between assigned read count and PCR Ct value
- review
- method: source-hash-verification; deterministic-table-parse; independent-cell-check; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-09; artifact sha256: cd3a80d785b78377e79960d0280667f98cba3305d68426fdfaf8efeecd4542d7; retrieval url: https://www.medrxiv.org/content/medrxiv/early/2022/01/21/2022.01.21.22269647/DC1/embed/media-1.xlsx; method note: Re-downloaded the workbook and matched its SHA-256. Read Carbo et al. Supplementary Table 1 (medRxiv v1 workbook) with a separate stdlib OOXML reader written for this review (the extractor's script was not run). Checked printed and numeric value, locator, metric, unit and direction from the headers, and the evaluation's configuration, protocol and dataset. Recomputed the ROC distance for every row.; note: Extracted by deterministic parse of the pinned XLSX cell XML (extract/extract_rna_pathogen.py), with row and column labels asserted. printed_value is the cell text, or the shortest decimal that round-trips to the stored number; displayed spreadsheet formatting was not applied. Pending independent review. Independent review 2026-10-09: value and identity match the source.