vsn
This is the development version of vsn; for the stable release version, see vsn.
Variance stabilization and calibration for microarray data
DOI: 10.18129/B9.bioc.vsn
Bioconductor version: Development (3.24)
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 [aut, cre], Anja von Heydebreck [aut], Dennis Kostka [ctb], David Kreil [ctb], Hans-Ulrich Klein [ctb], Robert Gentleman [ctb], Deepayan Sarkar [ctb], Gordon Smyth [ctb], Federal Ministry of Research, Technology and Space of Germany, DHGP [fnd]
Maintainer: Wolfgang Huber <wolfgang.huber at embl.org>
citation("vsn")):Wolfgang Huber, Anja von Heydebreck. vsn: Variance stabilization and calibration for microarray data. doi:10.18129/B9.bioc.vsn, R package version 3.81.1, https://bioconductor.org/packages/vsn.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | HTML | |
| Verifying and assessing the performance with simulated data | HTML | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Microarray, OneChannel, Preprocessing, Software, TwoChannel |
| Version | 3.81.1 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0.0), methods, Biobase |
| Imports | affy, limma, lattice, ggplot2 |
| System Requirements | |
| URL | https://github.com/Huber-group-EMBL/vsn https://huber-group-embl.github.io/vsn/ |
| Bug Reports | https://github.com/Huber-group-EMBL/vsn/issues |
See More
| Suggests | affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr, testthat, hexbin |
| Linking To | |
| Enhances | |
| Depends On Me | protGear, rnaseqGene, webbioc |
| Imports Me | arrayQualityMetrics, autonomics, bnem, DEP, Doscheda, ExpressionNormalizationWorkflow, lfproQC, MatrixQCvis, metaseqR2, MSnbase, NormalyzerDE, PRONE, pvca, SmartPhos, tilingArray |
| Suggests Me | adSplit, beadarray, DAPAR, DaparToolshed, DESeq2, estrogen, flowVS, ggbio, GlobalAncova, globaltest, limma, LIPIDIFy, lumi, MsCoreUtils, PAA, QFeatures, qmtools, ribosomeProfilingQC, scp, twilight, wrMisc |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | vsn_3.81.1.tar.gz |
| Windows Binary (x86_64) | vsn_3.81.1.zip |
| macOS Binary (big-sur-x86_64) | vsn_3.81.1.tgz |
| macOS Binary (sonoma-arm64) | vsn_3.81.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/vsn |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/vsn |
| Package Short Url | https://bioconductor.org/packages/vsn/ |
| Package Downloads Report | Download Stats |