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pvca

This is the development version of pvca; for the stable release version, see pvca.

Principal Variance Component Analysis (PVCA)

Bioconductor version: Development (3.18)

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 (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF R Script
Reference Manual PDF

Details

biocViews BatchEffect, Microarray, Software
Version 1.41.0
In Bioconductor since BioC 2.12 (R-3.0) (10.5 years)
License LGPL (>= 2.0)
Depends R (>= 2.15.1)
Imports Matrix, Biobase, vsn, stats, lme4
Linking To
Suggests golubEsets
System Requirements
Enhances
URL
See More
Depends On Me
Imports Me ExpressionNormalizationWorkflow
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package pvca_1.41.0.tar.gz
Windows Binary pvca_1.41.0.zip
macOS Binary (x86_64) pvca_1.41.0.tgz
macOS Binary (arm64) pvca_1.41.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/pvca
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pvca
Bioc Package Browser https://code.bioconductor.org/browse/pvca/
Package Short Url https://bioconductor.org/packages/pvca/
Package Downloads Report Download Stats