source("http://bioconductor.org/biocLite.R")
biocLite("pvca")

pvca

Principal Variance Component Analysis (PVCA)

Bioconductor version: 2.13

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 and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("pvca")

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		pvcaEstimate.pdf
PDF		Reference Manual

Details

biocViews	BatchEffectAssessment, Bioinformatics, Microarray, Software
Version	1.2.0
In Bioconductor since	BioC 2.12 (R-3.0)
License	LGPL (>= 2.0)
Depends	R (>= 2.15.1)
Imports	Matrix, Biobase, vsn, lme4
Suggests	golubEsets
System Requirements
URL
Depends On Me
Imports Me
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Package Archives

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

Package Source	pvca_1.2.0.tar.gz
Windows Binary	pvca_1.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	pvca_1.2.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats