pvca

Principal Variance Component Analysis (PVCA)

Bioconductor version: Release (2.14)

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("pvca")

Documentation

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

Details

biocViews BatchEffect, Microarray, Software
Version 1.4.0
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
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Package Downloads

Package Source pvca_1.4.0.tar.gz
Windows Binary pvca_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) pvca_1.4.0.tgz
Mac OS X 10.9 (Mavericks)
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