Package: puma
Type: Package
Title: Propagating Uncertainty in Microarray Analysis(including
        Affymetrix tranditional 3' arrays and exon arrays and Human
        Transcriptome Array 2.0)
Version: 3.54.0
Date: 2015-7-29
Author: Richard D. Pearson, Xuejun Liu, Magnus Rattray, Marta Milo,
        Neil D. Lawrence, Guido Sanguinetti, Li Zhang
Maintainer: Xuejun Liu <xuejun.liu@nuaa.edu.cn>
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
Suggests: pumadata, affydata, snow, limma, ROCR,annotate
Description: 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.
License: LGPL
biocViews: Microarray, OneChannel, Preprocessing,
        DifferentialExpression, Clustering, ExonArray, GeneExpression,
        mRNAMicroarray, ChipOnChip, AlternativeSplicing,
        DifferentialSplicing, Bayesian, TwoChannel, DataImport, HTA2.0
URL: http://umber.sbs.man.ac.uk/resources/puma
Packaged: 2026-04-29 23:59:45 UTC; root
NeedsCompilation: yes
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:32:24 UTC
RemoteUrl: https://github.com/bioc/puma
RemoteRef: RELEASE_3_23
RemoteSha: dbcf9141a6eb3dde4c864b3ccfd035841c107b23
Built: R 4.6.0; x86_64-apple-darwin20; 2026-04-30 00:04:24 UTC; unix
