vsn
This is the released version of vsn; for the devel version, see vsn.
Variance stabilization and calibration for microarray data
DOI: 10.18129/B9.bioc.vsn
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | HTML | |
| Verifying and assessing the performance with simulated data | HTML | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Microarray, OneChannel, Preprocessing, Software, TwoChannel |
| Version | 3.80.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21 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 |
| 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 | webbioc, rnaseqGene |
| Imports Me | arrayQualityMetrics, autonomics, bnem, Doscheda, MatrixQCvis, metaseqR2, MSnbase, NormalyzerDE, PRONE, pvca, SmartPhos, tilingArray, ExpressionNormalizationWorkflow, lfproQC |
| Suggests Me | adSplit, beadarray, DAPAR, DESeq2, ggbio, GlobalAncova, globaltest, limma, lumi, MsCoreUtils, PAA, QFeatures, 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_3.80.0.tar.gz |
| Windows Binary (x86_64) | vsn_3.80.0.zip |
| macOS Binary (big-sur-x86_64) | vsn_3.80.0.tgz |
| macOS Binary (sonoma-arm64) | vsn_3.80.0.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 |