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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("puma")
AuthorRichard D. Pearson, Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence, Guido Sanguinetti, Li Zhang
Bioconductor views AlternativeSplicing Bayesian ChipOnChip Clustering DataImport DifferentialExpression DifferentialSplicing ExonArray GeneExpression HTA2.0 Microarray OneChannel Preprocessing TwoChannel mRNAMicroarray
Date of publicationNone
MaintainerXuejun Liu <xuejun.liu@nuaa.edu.cn>
LicenseLGPL
Version3.18.0
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...

Functions

bcomb Man page
calcAUC Man page
calculateFC Man page
calculateLimma Man page
calculateTtest Man page
class:DEResult Man page
class:exprReslt Man page
class:pumaPCARes Man page
clusterApplyLBDots Man page
clusterNormE Man page
clusterNormVar Man page
Clust.exampleE Man page
Clust.exampleStd Man page
Clustii.exampleE Man page
Clustii.exampleStd Man page
compareLimmapumaDE Man page
createContrastMatrix Man page
createDesignMatrix Man page
create_eset_r Man page
DEMethod Man page
DEMethod<- Man page
DEMethod<-,DEResult,character-method Man page
DEMethod,DEResult-method Man page
DEResult Man page
DEResult-class Man page
erfc Man page
eset_mmgmos Man page
exampleE Man page
exampleStd Man page
exprReslt Man page
exprReslt-class Man page
FC Man page
FC<- Man page
FC<-,DEResult,matrix-method Man page
FC,DEResult-method Man page
gmhta Man page
gmoExon Man page
hcomb Man page
hgu95aphis Man page
igmoExon Man page
just.mgmos Man page
justmgMOS Man page
just.mmgmos Man page
justmmgMOS Man page
legend2 Man page
license.puma Man page
matrixDistance Man page
mgmos Man page
mmgmos Man page
newtonStep Man page
normalisation.gs Man page
numberOfContrasts Man page
numberOfContrasts,DEResult-method Man page
numberOfGenes Man page
numberOfGenes,DEResult-method Man page
numberOfProbesets Man page
numberOfProbesets,DEResult-method Man page
numFP Man page
numOfFactorsToUse Man page
numTP Man page
orig_pplr Man page
pLikeValues Man page
pLikeValues,DEResult-method Man page
plotErrorBars Man page
plotHistTwoClasses Man page
plot-methods Man page
plot.pumaPCARes Man page
plot,pumaPCARes-method Man page
plot,pumaPCARes,missing-method Man page
plotROC Man page
plotWhiskers Man page
PMmmgmos Man page
pplr Man page
pplrUnsorted Man page
prcfifty Man page
prcfifty<- Man page
prcfifty<-,exprReslt-method Man page
prcfifty,exprReslt-method Man page
prcfive Man page
prcfive<- Man page
prcfive<-,exprReslt-method Man page
prcfive,exprReslt-method Man page
prcninfive Man page
prcninfive<- Man page
prcninfive<-,exprReslt-method Man page
prcninfive,exprReslt-method Man page
prcsevfive Man page
prcsevfive<- Man page
prcsevfive<-,exprReslt-method Man page
prcsevfive,exprReslt-method Man page
prctwfive Man page
prctwfive<- Man page
prctwfive<-,exprReslt-method Man page
prctwfive,exprReslt-method Man page
puma Man page
pumaClust Man page
pumaClustii Man page
pumaComb Man page
pumaCombImproved Man page
pumaDE Man page
pumaDEUnsorted Man page
pumaFull Man page
pumaNormalize Man page
puma-package Man page
pumaPCA Man page
pumaPCAEstep Man page
pumaPCAExpectations Man page
pumaPCAExpectations-class Man page
pumaPCALikelihoodBound Man page
pumaPCALikelihoodCheck Man page
pumaPCAModel Man page
pumaPCAModel-class Man page
pumaPCANewtonUpdateLogSigma Man page
pumaPCARemoveRedundancy Man page
pumaPCARes Man page
pumaPCARes-class Man page
pumaPCASigmaGradient Man page
pumaPCASigmaObjective Man page
pumaPCAUpdateCinv Man page
pumaPCAUpdateM Man page
pumaPCAUpdateMu Man page
pumaPCAUpdateW Man page
removeUninformativeFactors Man page
se.exprs Man page
se.exprs<- Man page
se.exprs<-,exprReslt-method Man page
se.exprs,exprReslt-method Man page
show,DEResult-method Man page
show,exprReslt-method Man page
statistic Man page
statistic<- Man page
statistic<-,DEResult,matrix-method Man page
statistic,DEResult-method Man page
statisticDescription Man page
statisticDescription<- Man page
statisticDescription<-,DEResult,character-method Man page
statisticDescription,DEResult-method Man page
topGeneIDs Man page
topGeneIDs,DEResult-method Man page
topGenes Man page
topGenes,DEResult-method Man page
write.reslts Man page
write.reslts,DEResult-method Man page
write.reslts,ExpressionSet-method Man page
write.reslts,exprReslt-method Man page
write.reslts,pumaPCARes-method Man page

Files

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