pvca
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see pvca.
Principal Variance Component Analysis (PVCA)
Bioconductor version: 3.9
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("pvca")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("pvca")
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("pvca")| Batch effect estimation in Microarray data | R Script | |
| Reference Manual |
Details
| biocViews | BatchEffect, Microarray, Software |
| Version | 1.24.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (11 years) |
| License | LGPL (>= 2.0) |
| Depends | R (>= 2.15.1) |
| Imports | Matrix, Biobase, vsn, stats, lme4 |
| System Requirements | |
| URL |
See More
| Suggests | golubEsets |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | ExpressionNormalizationWorkflow, proBatch |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | pvca_1.24.0.tar.gz |
| Windows Binary | pvca_1.24.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | pvca_1.24.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/pvca |
| Source Repository (Developer Access) | git clone [email protected]:packages/pvca |
| Bioc Package Browser | https://code.bioconductor.org/browse/pvca/ |
| Package Short Url | https://bioconductor.org/packages/pvca/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |