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

Principal Variance Component Analysis (PVCA)

Bioconductor version: Development (3.19)

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 "4.4") and enter:

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

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews BatchEffect, Microarray, Software
Version 1.43.0
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
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Suggests golubEsets
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Imports Me ExpressionNormalizationWorkflow
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Follow Installation instructions to use this package in your R session.

Source Package pvca_1.43.0.tar.gz
Windows Binary pvca_1.43.0.zip (64-bit only)
macOS Binary (x86_64) pvca_1.43.0.tgz
macOS Binary (arm64) pvca_1.43.0.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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