puma

Propagating Uncertainty in Microarray Analysis

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
Maintainer Richard Pearson

To install this package, start R and enter:

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

Documentation

Package Downloads

puma.pdf
Reference Manual
Package source puma_1.8.1.tar.gz
Windows binary puma_1.8.1.zip
MacOS X 10.4 (Tiger) binary puma_1.8.1.tgz
MacOS X 10.5 (Leopard) binary puma_1.8.1.tgz
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Details

biocViews
Depends
R , Biobase , affy , graphics , grDevices , methods , stats , utils
Imports
Suggests
pumadata , affydata , snow , limma , annotate , ROCR
System Requirements
License LGPL excluding donlp2
URL http://umber.sbs.man.ac.uk/resources/puma
Depends On Me
Imports Me
Suggests Me
Development History Bioconductor Changelog