puma

Propagating Uncertainty in Microarray Analysis

Bioconductor version: Release (2.11)

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>

To install this package, start R and enter:

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

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

    citation("puma")

Documentation

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	3.0.0
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)
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