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

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.

AuthorRichard D. Pearson, Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence, Guido Sanguinetti, Li Zhang
Date of publicationNone
MaintainerXuejun Liu <xuejun.liu@nuaa.edu.cn>
LicenseLGPL
Version3.16.0
http://umber.sbs.man.ac.uk/resources/puma

View on Bioconductor

Man pages

bcomb: Combining replicates for each condition

calcAUC: Calculate Area Under Curve (AUC) for a standard ROC plot.

calculateFC: Calculate differential expression between conditions using FC

calculateLimma: Calculate differential expression between conditions using...

calculateTtest: Calculate differential expression between conditions using...

clusterApplyLBDots: clusterApplyLB with dots to indicate progress

clusterNormE: Zero-centered normalisation

clusterNormVar: Adjusting expression variance for zero-centered normalisation

Clust.exampleE: The example data of the mean gene expression levels

Clust.exampleStd: The example data of the standard deviation for gene...

Clustii.exampleE: The example data of the mean gene expression levels

Clustii.exampleStd: The example data of the standard deviation for gene...

compareLimmapumaDE: Compare pumaDE with a default Limma model

createContrastMatrix: Automatically create a contrast matrix from an ExpressionSet...

createDesignMatrix: Automatically create a design matrix from an ExpressionSet

create_eset_r: Create an ExpressionSet from a PPLR matrix

DEResult-class: Class DEResult

erfc: The complementary error function

eset_mmgmos: An example ExpressionSet created from the Dilution data with...

exampleE: The example data of the mean gene expression levels

exampleStd: The example data of the standard deviation for gene...

exprReslt-class: Class exprReslt

gmhta: Compute gene and transcript expression values and standard...

gmoExon: Compute gene and transcript expression values and standard...

hcomb: Combining replicates for each condition with the true gene...

hgu95aphis: Estimated parameters of the distribution of phi

igmoExon: Separately Compute gene and transcript expression values and...

justmgMOS: Compute mgmos Directly from CEL Files

justmmgMOS: Compute mmgmos Directly from CEL Files

legend2: A legend which allows longer lines

license.puma: Print puma license

matrixDistance: Calculate distance between two matrices

mgmos: modified gamma Model for Oligonucleotide Signal

mmgmos: Multi-chip modified gamma Model for Oligonucleotide Signal

normalisation.gs: Global scaling normalisation

numFP: Number of False Positives for a given proportion of True...

numOfFactorsToUse: Determine number of factors to use from an ExpressionSet

numTP: Number of True Positives for a given proportion of False...

orig_pplr: Probability of positive log-ratio

plotErrorBars: Plot mean expression levels and error bars for one or more...

plotHistTwoClasses: Stacked histogram plot of two different classes

plot-methods: Plot method for pumaPCARes objects

plotROC: Receiver Operator Characteristic (ROC) plot

plotWhiskers: Standard errors whiskers plot

PMmmgmos: Multi-chip modified gamma Model for Oligonucleotide Signal...

pplr: Probability of positive log-ratio

pplrUnsorted: Return an unsorted matrix of PPLR values

pumaclust: Propagate probe-level uncertainty in model-based clustering...

pumaClustii: Propagate probe-level uncertainty in robust t mixture...

pumaComb: Combining replicates for each condition

pumaCombImproved: Combining replicates for each condition with the true gene...

pumaDE: Calculate differential expression between conditions

pumaDEUnsorted: Return an unsorted matrix of PPLR values

pumaFull: Perform a full PUMA analysis

pumaNormalize: Normalize an ExpressionSet

puma-package: puma - Propagating Uncertainty in Microarray Analysis

pumaPCA: PUMA Principal Components Analysis

pumaPCAExpectations-class: Class pumaPCAExpectations

pumaPCAModel-class: Class pumaPCAModel

pumaPCARes-class: Class pumaPCARes

removeUninformativeFactors: Remove uninformative factors from the phenotype data of an...

Files in this package

puma/COPYING
puma/DESCRIPTION
puma/NAMESPACE
puma/R
puma/R/PMmmgmos.R puma/R/bcomb.R puma/R/calculateLimma.R puma/R/classes.R puma/R/compareLimmapumaDE.R puma/R/create_eset_r.R puma/R/esetFunctions.R puma/R/gmhta.R puma/R/gmoExon.R puma/R/hcomb.R puma/R/igmoExon.R puma/R/justmgmos.R puma/R/justmmgmos.R puma/R/matrixDistance.R puma/R/mgmos.R puma/R/mmgmos.R puma/R/numFP.R puma/R/orig_pplr.R puma/R/plotErrorBars.R puma/R/pplr.R puma/R/pumaClust.R puma/R/pumaClustii.R puma/R/pumaComb.R puma/R/pumaCombImproved.R puma/R/pumaDE.R puma/R/pumaFull.R puma/R/pumaPCA.R puma/R/pumaPCAEstep.R puma/R/pumaPCALikelihoodBound.R puma/R/pumaPCALikelihoodCheck.R puma/R/pumaPCANewtonUpdateLogSigma.R puma/R/pumaPCARemoveRedundancy.R puma/R/pumaPCASigmaGradient.R puma/R/pumaPCASigmaObjective.R puma/R/pumaPCAUpdateCinv.R puma/R/pumaPCAUpdateM.R puma/R/pumaPCAUpdateMu.R puma/R/pumaPCAUpdateW.R puma/R/pumaPlots.R puma/R/zzz.R
puma/build
puma/build/vignette.rds
puma/data
puma/data/Clust.exampleE.RData
puma/data/Clust.exampleStd.RData
puma/data/Clustii.exampleE.RData
puma/data/Clustii.exampleStd.RData
puma/data/datalist
puma/data/eset_mmgmos.rda
puma/data/exampleE.rda
puma/data/exampleStd.rda
puma/data/hgu95aphis.rda
puma/demo
puma/demo/00Index
puma/demo/puma.tour.R
puma/inst
puma/inst/CITATION
puma/inst/doc
puma/inst/doc/puma.R
puma/inst/doc/puma.Rnw
puma/inst/doc/puma.pdf
puma/man
puma/man/Clust.exampleE.Rd puma/man/Clust.exampleStd.Rd puma/man/Clustii.exampleE.Rd puma/man/Clustii.exampleStd.Rd puma/man/DEResult-class.Rd puma/man/PMmmgmos.Rd puma/man/bcomb.Rd puma/man/calcAUC.Rd puma/man/calculateFC.Rd puma/man/calculateLimma.Rd puma/man/calculateTtest.Rd puma/man/clusterApplyLBDots.Rd puma/man/clusterNormE.Rd puma/man/clusterNormVar.Rd puma/man/compareLimmapumaDE.Rd puma/man/createContrastMatrix.Rd puma/man/createDesignMatrix.Rd puma/man/create_eset_r.Rd puma/man/erfc.Rd puma/man/eset_mmgmos.Rd puma/man/exampleE.Rd puma/man/exampleStd.Rd puma/man/exprReslt-class.Rd puma/man/gmhta.Rd puma/man/gmoExon.Rd puma/man/hcomb.Rd puma/man/hgu95aphis.Rd puma/man/igmoExon.Rd puma/man/justmgMOS.Rd puma/man/justmmgMOS.Rd puma/man/legend2.Rd puma/man/license.puma.Rd puma/man/matrixDistance.Rd puma/man/mgmos.Rd puma/man/mmgmos.Rd puma/man/normalisation.gs.Rd puma/man/numFP.Rd puma/man/numOfFactorsToUse.Rd puma/man/numTP.Rd puma/man/orig_pplr.Rd puma/man/plot-methods.Rd puma/man/plotErrorBars.Rd puma/man/plotHistTwoClasses.Rd puma/man/plotROC.Rd puma/man/plotWhiskers.Rd puma/man/pplr.Rd puma/man/pplrUnsorted.Rd puma/man/puma-package.Rd puma/man/pumaClustii.Rd puma/man/pumaComb.Rd puma/man/pumaCombImproved.Rd puma/man/pumaDE.Rd puma/man/pumaDEUnsorted.Rd puma/man/pumaFull.Rd puma/man/pumaNormalize.Rd puma/man/pumaPCA.Rd puma/man/pumaPCAExpectations-class.Rd puma/man/pumaPCAModel-class.Rd puma/man/pumaPCARes-class.Rd puma/man/pumaclust.Rd puma/man/removeUninformativeFactors.Rd
puma/src
puma/src/PMmultimgmos.c
puma/src/PMmultimgmoshead.h
puma/src/cregistration.c
puma/src/donlp2.c
puma/src/global_constants.h
puma/src/gme.c
puma/src/gmehead.h
puma/src/ipplr_c.c
puma/src/ipplr_c.h
puma/src/multimgmos.c
puma/src/multimgmos.h
puma/src/newx.c
puma/src/o8comm.h
puma/src/o8cons.h
puma/src/o8fint.h
puma/src/o8fuco.h
puma/src/o8gene.h
puma/src/o8para.h
puma/src/pplr_c.c
puma/src/pplr_c.h
puma/src/pumaclust_c.c
puma/src/pumaclust_c.h
puma/src/pumaclustii_c.c
puma/src/pumaclustii_c.h
puma/src/user_eval.c
puma/vignettes
puma/vignettes/changelog.txt
puma/vignettes/puma-014.eps
puma/vignettes/puma-014.pdf
puma/vignettes/puma-015.eps
puma/vignettes/puma-015.pdf
puma/vignettes/puma-016.eps
puma/vignettes/puma-016.pdf
puma/vignettes/puma-022.eps
puma/vignettes/puma-022.pdf
puma/vignettes/puma-023.eps
puma/vignettes/puma-023.pdf
puma/vignettes/puma-024.eps
puma/vignettes/puma-024.pdf
puma/vignettes/puma.Rnw
puma/vignettes/puma.bib

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