vsn
Variance stabilization and calibration for microarray data
DOI: 10.18129/B9.bioc.vsn
Bioconductor version: Release (3.19)
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.
Author: Wolfgang Huber, with contributions from Anja von Heydebreck. Many comments and suggestions by users are acknowledged, among them Dennis Kostka, David Kreil, Hans-Ulrich Klein, Robert Gentleman, Deepayan Sarkar and Gordon Smyth
Maintainer: Wolfgang Huber <wolfgang.huber at embl.org>
citation("vsn")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("vsn")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("vsn")| Introduction to vsn (HTML version) | HTML | R Script |
| Likelihood Calculations for vsn | R Script | |
| Verifying and assessing the performance with simulated data | ||
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Microarray, OneChannel, Preprocessing, Software, TwoChannel |
| Version | 3.72.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 19.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0.0), methods, Biobase |
| Imports | affy, limma, lattice, ggplot2 |
| System Requirements | |
| URL | http://www.r-project.org http://www.ebi.ac.uk/huber |
See More
| Suggests | affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | cellHTS2, webbioc, rnaseqGene |
| Imports Me | DEP, Doscheda, MSnbase, MatrixQCvis, NormalyzerDE, arrayQualityMetrics, autonomics, bnem, metaseqR2, pvca, tilingArray, ExpressionNormalizationWorkflow, lfproQC |
| Suggests Me | DAPAR, DESeq2, GlobalAncova, MsCoreUtils, PAA, QFeatures, adSplit, beadarray, ggbio, globaltest, limma, lumi, qmtools, ribosomeProfilingQC, scp, twilight, estrogen, wrMisc |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | vsn_3.72.0.tar.gz |
| Windows Binary (x86_64) | vsn_3.72.0.zip |
| macOS Binary (x86_64) | vsn_3.72.0.tgz |
| macOS Binary (arm64) | vsn_3.72.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/vsn |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/vsn |
| Bioc Package Browser | https://code.bioconductor.org/browse/vsn/ |
| Package Short Url | https://bioconductor.org/packages/vsn/ |
| Package Downloads Report | Download Stats |