pvca
Principal Variance Component Analysis (PVCA)
Bioconductor version: Release (2.12)
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
| R Script | Batch effect estimation in Microarray data | |
| pvcaEstimate.pdf | ||
| Reference Manual |
Details
| biocViews | BatchEffectAssessment, Bioinformatics, Microarray, Software |
| Version | 1.0.1 |
| In Bioconductor since | BioC 2.13 (R-2.18) |
| License | LGPL (>= 2.0) |
| Depends | R (>= 2.15.1) |
| Imports | Matrix, Biobase, vsn, lme4 |
| Suggests | golubEsets |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Downloads
| Package Source | pvca_1.0.1.tar.gz |
| Windows Binary | pvca_1.0.1.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | pvca_1.0.1.tgz |
| Package Downloads Report | Download Stats |
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