DOI: 10.18129/B9.bioc.pvca  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see pvca.

Principal Variance Component Analysis (PVCA)

Bioconductor version: 3.16

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")):


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


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


biocViews BatchEffect, Microarray, Software
Version 1.38.0
In Bioconductor since BioC 2.12 (R-3.0) (10 years)
License LGPL (>= 2.0)
Depends R (>= 2.15.1)
Imports Matrix, Biobase, vsn, stats, lme4
Suggests golubEsets
Depends On Me
Imports Me ExpressionNormalizationWorkflow, proBatch
Suggests Me
Links To Me
Build Report  

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

Source Package pvca_1.38.0.tar.gz
Windows Binary pvca_1.38.0.zip
macOS Binary (x86_64) pvca_1.38.0.tgz
macOS Binary (arm64) pvca_1.38.0.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/
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