pcaMethods

A collection of PCA methods.

Bioconductor version: Release (2.7)

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 unique interface to the PCA results. Initiated at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany. Now developed at CAS-MPG Partner Institute for Computational Biology (PICB) Shanghai, P.R. China and RIKEN Plant Science Center, Yokohama Japan.

Author: Wolfram Stacklies, Henning Redestig, Kevin Wright

Maintainer: Wolfram Stacklies

To install this package, start R and enter:

source("http:///biocLite.R")
biocLite("pcaMethods")    

Documentation

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

Reference Manual

Details

biocViews	Bioinformatics
Depends	Biobase, MASS, pls, methods, Rcpp
Imports
Suggests	aroma.light
System Requirements	Rcpp
License	GPL (>= 3)
URL
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Version	1.32.0

Package Downloads

Package Source	pcaMethods_1.32.0.tar.gz
Windows Binary	pcaMethods_1.32.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	pcaMethods_1.32.0.tgz
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