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