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Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

Bioconductor version: Release (3.19)

Most analyses of Affymetrix GeneChip data (including tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0) 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. In additon to calculte gene expression from Affymetrix 3' arrays, puma also provides methods to process exon arrays and produces gene and isoform expression for alternative splicing study. 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 functions.

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

Maintainer: Xuejun Liu <xuejun.liu at>

Citation (from within R, enter citation("puma")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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

puma User Guide PDF R Script
Reference Manual PDF


biocViews AlternativeSplicing, Bayesian, ChipOnChip, Clustering, DataImport, DifferentialExpression, DifferentialSplicing, ExonArray, GeneExpression, HTA2.0, Microarray, OneChannel, Preprocessing, Software, TwoChannel, mRNAMicroarray
Version 3.46.0
In Bioconductor since BioC 2.0 (R-2.5) (17 years)
License LGPL
Depends R (>= 3.2.0), oligo(>= 1.32.0), graphics, grDevices, methods, stats, utils, mclust, oligoClasses
Imports Biobase(>= 2.5.5), affy(>= 1.46.0), affyio, oligoClasses
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Suggests pumadata, affydata, snow, limma, ROCR, annotate
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Source Package puma_3.46.0.tar.gz
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