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

puma

Propagating Uncertainty in Microarray Analysis

Bioconductor version: 2.13

Most analyses of Affymetrix GeneChip data are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting and data manipulation functions.

Author: Richard D. Pearson, Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence, Guido Sanguinetti, Li Zhang

Maintainer: Richard Pearson <richard.pearson at well.ox.ac.uk>

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("puma")

 

PDF		puma-014.pdf
PDF		puma-015.pdf
PDF		puma-016.pdf
PDF		puma-022.pdf
PDF		puma-023.pdf
PDF		puma-024.pdf
PDF		puma.pdf
PDF		Reference Manual

Details

biocViews	Bioinformatics, Clustering, DifferentialExpression, Microarray, OneChannel, Preprocessing, Software
Version	3.4.0
In Bioconductor since	BioC 2.0 (R-2.5)
License	LGPL
Depends	R (>= 2.10), Biobase(>= 2.5.5), affy(>= 1.23.4), graphics, grDevices, methods, stats, utils, mclust
Imports	Biobase(>= 2.5.5), affy(>= 1.23.4), affyio
Suggests	pumadata, affydata, snow, limma, annotate, ROCR
System Requirements
URL	http://umber.sbs.man.ac.uk/resources/puma
Depends On Me	pumadata
Imports Me	tigre
Suggests Me	tigre

Package Archives

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

Package Source	puma_3.4.0.tar.gz
Windows Binary	puma_3.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	puma_3.4.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats