To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("pvca")
In most cases, you don't need to download the package archive at all.
pvca
|
This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see pvca.
Principal Variance Component Analysis (PVCA)
Bioconductor version: 2.12
This package contains the function to assess the batch sourcs by fitting all "sources" as random effects including two-way interaction terms in the Mixed Model(depends on lme4 package) to selected principal components, which were obtained from the original data correlation matrix. This package accompanies the book "Batch Effects and Noise in Microarray Experiements, chapter 12.
Author: Pierre Bushel <bushel at niehs.nih.gov>
Maintainer: Jianying LI <li11 at niehs.nih.gov>
Citation (from within R,
enter citation("pvca")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("pvca")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("pvca")
| R Script | Batch effect estimation in Microarray data | |
| pvcaEstimate.pdf | ||
| Reference Manual |
Details
| biocViews | BatchEffectAssessment, Bioinformatics, Microarray, Software |
| Version | 1.0.1 |
| In Bioconductor since | BioC 2.12 (R-3.0) (3 years) |
| License | LGPL (>= 2.0) |
| Depends | R (>= 2.15.1) |
| Imports | Matrix, Biobase, vsn, lme4 |
| LinkingTo | |
| Suggests | golubEsets |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | pvca_1.0.1.tar.gz |
| Windows Binary | pvca_1.0.1.zip |
| Mac OS X 10.6 (Snow Leopard) | pvca_1.0.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/pvca/tree/release-2.12 |
| Package Short Url | http://bioconductor.org/packages/pvca/ |
| Package Downloads Report | Download Stats |
Documentation »
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