vsn
Bioc currentVariance stabilization and calibration for microarray data
Release Lineage
Entered 1.4 · May 17, 2004
Current · Requires R 4.6
Description
The package implements a method for normalising microarray intensities from single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
53 7 exported
Complexity
5.3 avg / 22 max
Call network
53 nodes / 50 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
5,027
Files
56
Compiled share
21.8%
Has compiled src
Yes
Language breakdown
API
Exported functions
7
Internal functions
30
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.01
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
45
First release
2004-08-23
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
12
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 13includes a package overview page
- Examples that run
- 91%10 run in a plain check · 1 hold no code
- Exported functions with examples
- 100%
- Documented parameters
- 90%
- Return-value docs
- 100%
- Help pages citing references
- 31%
Repository practices
6 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/huber-group-embl/vsn on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-09-23 · The repository has a site deploy workflow
Datasets
Topics
Depended on by (28)
Show all 51 packagesHide all 51 packages
Bioconductor (27)
CRAN (1)
People
- Wolfgang Huber author maintainer
- Federal Ministry of Research, Technology and Space of Germany, DHGP funder
- Robert Gentleman contributor
- Hans-Ulrich Klein contributor
- Dennis Kostka contributor
- David Kreil contributor
- Deepayan Sarkar contributor
- Gordon Smyth contributor
- Anja von Heydebreck author
Cite
Cite this package
Run in R for the authors' entry:
citation("vsn")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/18.suppl_1.s96.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.