pvca

DOI: 10.18129/B9.bioc.pvca    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see pvca.

Principal Variance Component Analysis (PVCA)

Bioconductor version: 3.11

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

PDF	R Script	Batch effect estimation in Microarray data
PDF		Reference Manual

Details

biocViews	BatchEffect, Microarray, Software
Version	1.28.0
In Bioconductor since	BioC 2.12 (R-3.0) (7.5 years)
License	LGPL (>= 2.0)
Depends	R (>= 2.15.1)
Imports	Matrix, Biobase, vsn, stats, lme4
LinkingTo
Suggests	golubEsets
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	ExpressionNormalizationWorkflow, proBatch
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	pvca_1.28.0.tar.gz
Windows Binary	pvca_1.28.0.zip
macOS 10.13 (High Sierra)	pvca_1.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/pvca
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/pvca
Package Short Url	https://bioconductor.org/packages/pvca/
Package Downloads Report	Download Stats