Registration Open for Bioc2024 July 24-26


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

A collection of PCA methods

Bioconductor version: Development (3.20)

Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results. Initiated at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany.

Author: Wolfram Stacklies, Henning Redestig, Kevin Wright

Maintainer: Henning Redestig < at>

Citation (from within R, enter citation("pcaMethods")):


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:

Data with outliers PDF R Script
Introduction PDF R Script
Missing value imputation PDF R Script
Reference Manual PDF


biocViews Bayesian, Software
Version 1.97.0
In Bioconductor since BioC 1.9 (R-2.4) (18 years)
License GPL (>= 3)
Depends Biobase, methods
Imports BiocGenerics, Rcpp (>= 0.11.3), MASS
System Requirements Rcpp
Bug Reports
See More
Suggests matrixStats, lattice, ggplot2
Linking To Rcpp
Depends On Me DeconRNASeq, crmn, DiffCorr, imputeLCMD
Imports Me consensusDE, destiny, FRASER, MAI, MatrixQCvis, MSnbase, MSPrep, MultiBaC, OUTRIDER, PhosR, pmp, scde, SomaticSignatures, ADAPTS, CopSens, geneticae, lfproQC, LOST, MetabolomicsBasics, missCompare, multiDimBio, pmartR, polyRAD, promor, RAMClustR, santaR, scMappR
Suggests Me autonomics, cardelino, MsCoreUtils, QFeatures, qmtools, mtbls2, pagoda2, rsvddpd
Links To Me
Build Report Build Report

Package Archives

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

Source Package pcaMethods_1.97.0.tar.gz
Windows Binary
macOS Binary (x86_64) pcaMethods_1.97.0.tgz
macOS Binary (arm64) pcaMethods_1.97.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats