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

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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
Date of publication
None
Maintainer
Xuejun Liu <xuejun.liu@nuaa.edu.cn>
License
LGPL
Version
3.16.0
URLs

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