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
gmoExon	gmoExon
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
PMmmgmos	PMmmgmos
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
