Gplots Package
Documentation reproduced from package gplots, version 3.1.1, License: GPL-2 Community examples. Looks like there are no examples yet. Post a new example: Submit your. Jan 31, 2013 Type “install.packages(“gplots”)” and then press the Enter/Return key. If you have already loaded a package from a server in the R session, then R will automatically install the package. If not, R will automatically prompt you to choose a mirror. I was using ubuntu 14.04.2 LTS. My R version was 3.0.2. When I used the following command to install package 'gplots' sudo -i R install.packages('gplots') I got a warning message: package ‘gplot.
- Install Package Gplots
- Gplots: Various R Programming Tools For Plotting Data Version ...
- How To Solve Gplots Installing Package Problem In R? - Stack ...
- Gplots Package R Install
Variance stabilization and calibration for microarray data
Bioconductor version: Release (3.12)
The package implements a method for normalising microarray intensities, and works for 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.de>
Citation (from within R, enter citation('vsn')):
Installation
To install this package, start R (version '4.0') and enter:
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:
| HTML | R Script | Introduction to vsn (HTML version) |
| R Script | Likelihood Calculations for vsn | |
| Verifying and assessing the performance with simulated data | ||
| Reference Manual | ||
| Text | NEWS |
Details
Install Package Gplots
| biocViews | Microarray, OneChannel, Preprocessing, Software, TwoChannel |
| Version | 3.58.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 15.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.4.0), Biobase |
| Imports | methods, affy, limma, lattice, ggplot2 |
| LinkingTo | |
| Suggests | affydata, hgu95av2cdf, BiocStyle, knitr, dplyr, testthat |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | affyPara, cellHTS2, MmPalateMiRNA, rnaseqGene, webbioc |
| Imports Me | arrayQualityMetrics, coexnet, DAPAR, DEP, Doscheda, ExpressionNormalizationWorkflow, imageHTS, metaseqR, metaseqR2, MSnbase, NormalyzerDE, pvca, Ringo, tilingArray |
| Suggests Me | adSplit, beadarray, BiocCaseStudies, DESeq, DESeq2, estrogen, flowVS, ggbio, GlobalAncova, globaltest, limma, lumi, MsCoreUtils, PAA, QFeatures, twilight |
| Links To Me | |
| Build Report |
Gplots: Various R Programming Tools For Plotting Data Version ...
Package Archives
How To Solve Gplots Installing Package Problem In R? - Stack ...
Follow Installation instructions to use this package in your R session.
Gplots Package R Install
| Source Package | vsn_3.58.0.tar.gz |
| Windows Binary | vsn_3.58.0.zip |
| macOS 10.13 (High Sierra) | vsn_3.58.0.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 |