Validation / Papers / Hahne 2009

flowCore: a Bioconductor package for high throughput flow cytometry

Flow cytometry · tool tutorial or software test data · flowCore (R), through the flowcore adapter

How to read this page. In this validation, a script plays the scientist. It gives the answers that we wrote before the run, from the methods of the paper. A known value comes from the paper, from a tutorial or from a check that we ran. This page has no combined run of the paper yet.

No run is scored for this paper yet.

The paper

Hahne F, LeMeur N, Brinkman RR, Ellis B, Haaland P, Sarkar D, Spidlen J, Strain E, Gentleman R. flowCore: a Bioconductor package for high throughput flow cytometry. BMC Bioinformatics 10:106 (2009). doi:10.1186/1471-2105-10-106

Related sources:

Data and reference matrix: the data set compdata in the Bioconductor package flowCore 2.24.0 (extdata/compdata), Artistic-2.0. Ellis B et al., flowCore, DOI 10.18129/B9.bioc.flowCore. doi:10.18129/B9.bioc.flowCore

What it measured

The data set compdata holds an unstained control and four single-stain controls (FL1-H to FL4-H) of one experiment on a BD instrument that writes log-amplified channel numbers. The flowCore package stores the spillover matrix of this experiment (compref) as the result of its own tests. A spillover coefficient is the median shift of a channel in the positive events of a control, divided by the median shift of the primary channel of that control.

Data

The data set compdata of flowCore 2.24.0 (extdata/compdata/data/060909.001 to 060909.005). fetch.sh copies the files from the installed package and keeps the reference matrix compref in the reference folder. Size: 660 KB for 5 FCS files with 7500 to 10000 events.

License: Artistic-2.0, the license of flowCore

Data source

The instruction

A script sends this message as the scientist.

ScientistCompute the spillover matrix from the controls and give the 12 off-diagonal coefficients.

Basis: The compdata files, the file comp_match (which file holds which control), and the reference matrix compref of the package.

The decisions

The model asks questions during a run. A script gives these answers to the questions of the model. We wrote the answers before the run.

**Table 1 |** Answers that a script gives to the questions of the model.
Decision	Value	Source
Cutoff for positive events in a control	`80`	Not in the package text. The percentiles 50 to 80 of the unstained control reproduce compref within 0.0004 (check_spillover.out). The 99th percentile differs by 0.008.
Decades of a log-amplified scale	`4`	The files hold log-amplified channel numbers of 1024 channels over four decades. Linear values are 10 to the power of (value divided by 256).
Parent gate on scatter	`none`	Not in the package text. The reference matrix uses all events.
Compensation of the samples	`none`	Not used. The benchmark makes the matrix only.
Transform of the fluorescence channels	`none`	Not used.
Cofactor of the asinh transform	`150`	Not used.
Cutoff between negative and positive	`none`	Not used.
Percentile of the control for the cutoff	`99`	Not used.
Statistical test for the groups	`welch`	Not used.
Correction for many comparisons	`holm`	Not used.
Other questions of the agent	`Use the values in the decision record.`	Not in the package text. The benchmark answers each free question with this text, so that the record of decisions stays the only source of the settings.

Known values

The tolerance is the largest difference from the known value that we accept. We set it before the run. Exact: the number must be the same.

**Table 2 |** Known values for Hahne 2009.
Value	Known value	Tolerance	Source
`spill_fl1_to_fl2`Spillover of the FL1-H control into FL2-H Source of the known value Printed in the official tutorialWhere: R package flowCore 2.24.0, extdata/compdata/compref, the reference matrix of the flowCore tests (row FL1-H, column FL2-H).Check: check_spillover.py recomputes the matrix with NumPy and flowio (check_spillover.out).Note in the list of known values: flowCore compref	0.242022	± 5e-05	Printed in the official tutorial
`spill_fl1_to_fl3`Spillover of the FL1-H control into FL3-H Source of the known value Printed in the official tutorialWhere: R package flowCore 2.24.0, extdata/compdata/compref, the reference matrix of the flowCore tests (row FL1-H, column FL3-H).Check: check_spillover.py recomputes the matrix with NumPy and flowio (check_spillover.out).Note in the list of known values: flowCore compref	0.032084	± 0.0004	Printed in the official tutorial
`spill_fl1_to_fl4`Spillover of the FL1-H control into FL4-H Source of the known value Printed in the official tutorialWhere: R package flowCore 2.24.0, extdata/compdata/compref, the reference matrix of the flowCore tests (row FL1-H, column FL4-H).Check: check_spillover.py recomputes the matrix with NumPy and flowio (check_spillover.out).Note in the list of known values: flowCore compref	0.001128	± 5e-05	Printed in the official tutorial
`spill_fl2_to_fl1`Spillover of the FL2-H control into FL1-H Source of the known value Printed in the official tutorialWhere: R package flowCore 2.24.0, extdata/compdata/compref, the reference matrix of the flowCore tests (row FL2-H, column FL1-H).Check: check_spillover.py recomputes the matrix with NumPy and flowio (check_spillover.out).Note in the list of known values: flowCore compref	0.007722	± 5e-05	Printed in the official tutorial
`spill_fl2_to_fl3`Spillover of the FL2-H control into FL3-H Source of the known value Printed in the official tutorialWhere: R package flowCore 2.24.0, extdata/compdata/compref, the reference matrix of the flowCore tests (row FL2-H, column FL3-H).Check: check_spillover.py recomputes the matrix with NumPy and flowio (check_spillover.out).Note in the list of known values: flowCore compref	0.140788	± 5e-05	Printed in the official tutorial
`spill_fl2_to_fl4`Spillover of the FL2-H control into FL4-H Source of the known value Printed in the official tutorialWhere: R package flowCore 2.24.0, extdata/compdata/compref, the reference matrix of the flowCore tests (row FL2-H, column FL4-H).Check: check_spillover.py recomputes the matrix with NumPy and flowio (check_spillover.out).Note in the list of known values: flowCore compref	0.002633	± 0.0002	Printed in the official tutorial
`spill_fl3_to_fl1`Spillover of the FL3-H control into FL1-H Source of the known value Printed in the official tutorialWhere: R package flowCore 2.24.0, extdata/compdata/compref, the reference matrix of the flowCore tests (row FL3-H, column FL1-H).Check: check_spillover.py recomputes the matrix with NumPy and flowio (check_spillover.out).Note in the list of known values: flowCore compref	0.015081	± 5e-05	Printed in the official tutorial
`spill_fl3_to_fl2`Spillover of the FL3-H control into FL2-H Source of the known value Printed in the official tutorialWhere: R package flowCore 2.24.0, extdata/compdata/compref, the reference matrix of the flowCore tests (row FL3-H, column FL2-H).Check: check_spillover.py recomputes the matrix with NumPy and flowio (check_spillover.out).Note in the list of known values: flowCore compref	0.17559	± 5e-05	Printed in the official tutorial
`spill_fl3_to_fl4`Spillover of the FL3-H control into FL4-H Source of the known value Printed in the official tutorialWhere: R package flowCore 2.24.0, extdata/compdata/compref, the reference matrix of the flowCore tests (row FL3-H, column FL4-H).Check: check_spillover.py recomputes the matrix with NumPy and flowio (check_spillover.out).Note in the list of known values: flowCore compref	0.229594	± 5e-05	Printed in the official tutorial
`spill_fl4_to_fl1`Spillover of the FL4-H control into FL1-H Source of the known value Printed in the official tutorialWhere: R package flowCore 2.24.0, extdata/compdata/compref, the reference matrix of the flowCore tests (row FL4-H, column FL1-H).Check: check_spillover.py recomputes the matrix with NumPy and flowio (check_spillover.out).Note in the list of known values: flowCore compref	0.000759	± 5e-05	Printed in the official tutorial
`spill_fl4_to_fl2`Spillover of the FL4-H control into FL2-H Source of the known value Printed in the official tutorialWhere: R package flowCore 2.24.0, extdata/compdata/compref, the reference matrix of the flowCore tests (row FL4-H, column FL2-H).Check: check_spillover.py recomputes the matrix with NumPy and flowio (check_spillover.out).Note in the list of known values: flowCore compref	0.000962	± 5e-05	Printed in the official tutorial
`spill_fl4_to_fl3`Spillover of the FL4-H control into FL3-H Source of the known value Printed in the official tutorialWhere: R package flowCore 2.24.0, extdata/compdata/compref, the reference matrix of the flowCore tests (row FL4-H, column FL3-H).Check: check_spillover.py recomputes the matrix with NumPy and flowio (check_spillover.out).Note in the list of known values: flowCore compref	0.003219	± 5e-05	Printed in the official tutorial

Latest scored run

No run is scored for this paper yet.

Notes

Triage notes by the maintainers

The text below is from the triage notes. We show it as the maintainers wrote it.

Classes: a = tool or adapter fault, b = harness fault, c = benchmark spec fault, d = model fault.

claude-haiku-5-5 run 1 (blind): computed 12/12, reported 12/12, 69 s, 0 paths outside the allow list.

Run	Item	Expected	Got	Class	Cause	Fix
1	none				No item failed.	none

Other findings:

The model gave 2 or 3 significant digits in the answer. The rounding rule accepted 0.141, 0.015, 0.176 and 0.23 for tolerances of 0.00005. The computed score reads the exact tool values (0.1407882 and others).
The tolerance of two items is larger (0.0004 for FL1-H into FL3-H and 0.0002 for FL2-H into FL4-H). The tool and the flowCore reference differ there (0.032409 against 0.032084, and 0.002740 against 0.002633). The reference comes from the flowStats code of 2009, which picks the positive events in a different way.