xps-package	xps-package
addData	addData-methods
addData,DataTreeSet-method	DataTreeSet-class
addData-methods	addData-methods
AnalysisTreeSet	AnalysisTreeSet-class
AnalysisTreeSet-class	AnalysisTreeSet-class
arrayInfo	ProjectInfo-class
arrayInfo,ProjectInfo-method	ProjectInfo-class
arrayInfo<-	ProjectInfo-class
arrayInfo<-,ProjectInfo,character-method	ProjectInfo-class
attachBgrd	attachBgrd-methods
attachBgrd,DataTreeSet-method	DataTreeSet-class
attachBgrd-methods	attachBgrd-methods
attachCall	attachCall-methods
attachCall,CallTreeSet-method	CallTreeSet-class
attachCall-methods	attachCall-methods
attachExpr	attachExpr-methods
attachExpr,ExprTreeSet-method	ExprTreeSet-class
attachExpr-methods	attachExpr-methods
attachInten	attachInten-methods
attachInten,DataTreeSet-method	DataTreeSet-class
attachInten-methods	attachInten-methods
attachMask	attachMask-methods
attachMask,DataTreeSet-method	DataTreeSet-class
attachMask,SchemeTreeSet-method	SchemeTreeSet-class
attachMask-methods	attachMask-methods
attachPVal	attachCall-methods
attachPVal,CallTreeSet-method	CallTreeSet-class
attachPVal-methods	attachCall-methods
authorInfo	ProjectInfo-class
authorInfo,ProjectInfo-method	ProjectInfo-class
authorInfo<-	ProjectInfo-class
authorInfo<-,ProjectInfo,character-method	ProjectInfo-class
background	DataTreeSet-class
background,DataTreeSet-method	DataTreeSet-class
background<-	DataTreeSet-class
background<-,DataTreeSet,data.frame-method	DataTreeSet-class
bgcorrect	bgcorrect
bgcorrect.gc	bgcorrect
bgcorrect.mas4	bgcorrect
bgcorrect.mas5	bgcorrect
bgcorrect.rma	bgcorrect
bgtreeNames	DataTreeSet-class
bgtreeNames,DataTreeSet-method	DataTreeSet-class
biopsyInfo	ProjectInfo-class
biopsyInfo,ProjectInfo-method	ProjectInfo-class
biopsyInfo<-	ProjectInfo-class
biopsyInfo<-,ProjectInfo,character-method	ProjectInfo-class
boxplot	boxplot-methods
boxplot,ProcesSet-method	ProcesSet-class
boxplot-methods	boxplot-methods
boxplot.dev	boxplot.dev
callFilter	callFilter-methods
callFilter,PreFilter-method	PreFilter-class
callFilter,UniFilter-method	UniFilter-class
callFilter-methods	callFilter-methods
callFilter<-	callFilter-methods
callFilter<-,PreFilter,character-method	PreFilter-class
callFilter<-,UniFilter,character-method	UniFilter-class
callplot	callplot-methods
callplot,CallTreeSet-method	CallTreeSet-class
callplot-methods	callplot-methods
CallTreeSet	CallTreeSet-class
callTreeset	FilterTreeSet-class
callTreeset,FilterTreeSet-method	FilterTreeSet-class
CallTreeSet-class	CallTreeSet-class
cellineInfo	ProjectInfo-class
cellineInfo,ProjectInfo-method	ProjectInfo-class
cellineInfo<-	ProjectInfo-class
cellineInfo<-,ProjectInfo,character-method	ProjectInfo-class
chipMask	SchemeTreeSet-class
chipMask,SchemeTreeSet-method	SchemeTreeSet-class
chipMask<-	SchemeTreeSet-class
chipMask<-,SchemeTreeSet,data.frame-method	SchemeTreeSet-class
chipName	SchemeTreeSet-class
chipName,ProcesSet-method	ProcesSet-class
chipName,SchemeTreeSet-method	SchemeTreeSet-class
chipType	SchemeTreeSet-class
chipType,ProcesSet-method	ProcesSet-class
chipType,SchemeTreeSet-method	SchemeTreeSet-class
chipType<-	SchemeTreeSet-class
chipType<-,SchemeTreeSet,character-method	SchemeTreeSet-class
cvFilter	cvFilter-methods
cvFilter,PreFilter-method	PreFilter-class
cvFilter-methods	cvFilter-methods
cvFilter<-	cvFilter-methods
cvFilter<-,PreFilter,numeric-method	PreFilter-class
dabg.call	dabg.call
datasetInfo	ProjectInfo-class
datasetInfo,ProjectInfo-method	ProjectInfo-class
datasetInfo<-	ProjectInfo-class
datasetInfo<-,ProjectInfo,character-method	ProjectInfo-class
DataTreeSet	DataTreeSet-class
DataTreeSet-class	DataTreeSet-class
debug.xps	xpsOptions
dfw	dfw
diffFilter	diffFilter-methods
diffFilter,PreFilter-method	PreFilter-class
diffFilter-methods	diffFilter-methods
diffFilter<-	diffFilter-methods
diffFilter<-,PreFilter,numeric-method	PreFilter-class
existsROOTFile	existsROOTFile
exonLevel	exonLevel
export	export
export,ProcesSet-method	ProcesSet-class
export,SchemeTreeSet-method	SchemeTreeSet-class
export,TreeSet-method	TreeSet-class
export-methods	export
export.call	export
export.data	export
export.expr	export
export.filter	export.filter
export.root	export.root
export.scheme	export
express	express
exprs	exprs-methods
exprs,ExprTreeSet-method	ExprTreeSet-class
exprs-methods	exprs-methods
exprs<-	exprs-methods
exprs<-,ExprTreeSet,data.frame-method	ExprTreeSet-class
ExprTreeSet	ExprTreeSet-class
exprTreeset	FilterTreeSet-class
exprTreeset,FilterTreeSet-method	FilterTreeSet-class
ExprTreeSet-class	ExprTreeSet-class
exprType	ExprTreeSet-class
exprType,ExprTreeSet-method	ExprTreeSet-class
exprType<-	ExprTreeSet-class
exprType<-,ExprTreeSet,character-method	ExprTreeSet-class
farms	farms
fcFilter	fcFilter-methods
fcFilter,UniFilter-method	UniFilter-class
fcFilter-methods	fcFilter-methods
fcFilter<-	fcFilter-methods
fcFilter<-,UniFilter,character-method	UniFilter-class
fileDir	TreeSet-class
fileDir,TreeSet-method	TreeSet-class
fileDir<-	TreeSet-class
fileDir<-,TreeSet,character-method	TreeSet-class
Filter-class	Filter-class
FilterTreeSet	FilterTreeSet-class
filterTreeset	AnalysisTreeSet-class
filterTreeset,AnalysisTreeSet-method	AnalysisTreeSet-class
FilterTreeSet-class	FilterTreeSet-class
gapFilter	gapFilter-methods
gapFilter,PreFilter-method	PreFilter-class
gapFilter-methods	gapFilter-methods
gapFilter<-	gapFilter-methods
gapFilter<-,PreFilter,numeric-method	PreFilter-class
getChipName	getChipName
getChipType	getChipType
getDatatype	getDatatype
getNameType	getNameType
getNumberTrees	getNumberTrees
getProbeInfo	getProbeInfo
getTreeData	getTreeData-methods
getTreeData,AnalysisTreeSet-method	AnalysisTreeSet-class
getTreeData,FilterTreeSet-method	FilterTreeSet-class
getTreeData,ProcesSet-method	ProcesSet-class
getTreeData-methods	getTreeData-methods
getTreeNames	getTreeNames
highFilter	highFilter-methods
highFilter,PreFilter-method	PreFilter-class
highFilter-methods	highFilter-methods
highFilter<-	highFilter-methods
highFilter<-,PreFilter,character-method	PreFilter-class
hist	hist-methods
hist,ProcesSet-method	ProcesSet-class
hist-methods	hist-methods
hybridizInfo	ProjectInfo-class
hybridizInfo,ProjectInfo-method	ProjectInfo-class
hybridizInfo<-	ProjectInfo-class
hybridizInfo<-,ProjectInfo,character-method	ProjectInfo-class
image	image-methods
image,DataTreeSet-method	DataTreeSet-class
image-methods	image-methods
image.dev	image.dev
import.data	import.data
import.exon.scheme	import.exon.scheme
import.expr.scheme	import.expr.scheme
import.genome.scheme	import.genome.scheme
ini.call	ini.call
initialize	initialize-methods
initialize,AnalysisTreeSet-method	initialize-methods
initialize,CallTreeSet-method	initialize-methods
initialize,DataTreeSet-method	initialize-methods
initialize,ExprTreeSet-method	initialize-methods
initialize,Filter-method	initialize-methods
initialize,FilterTreeSet-method	initialize-methods
initialize,PreFilter-method	initialize-methods
initialize,ProcesSet-method	initialize-methods
initialize,ProjectInfo-method	initialize-methods
initialize,SchemeTreeSet-method	initialize-methods
initialize,TreeSet-method	initialize-methods
initialize,UniFilter-method	initialize-methods
initialize-methods	initialize-methods
intensity	DataTreeSet-class
intensity,DataTreeSet-method	DataTreeSet-class
intensity<-	DataTreeSet-class
intensity<-,DataTreeSet,data.frame-method	DataTreeSet-class
isROOTFile	isROOTFile
lowFilter	lowFilter-methods
lowFilter,PreFilter-method	PreFilter-class
lowFilter-methods	lowFilter-methods
lowFilter<-	lowFilter-methods
lowFilter<-,PreFilter,character-method	PreFilter-class
madFilter	madFilter-methods
madFilter,PreFilter-method	PreFilter-class
madFilter-methods	madFilter-methods
madFilter<-	madFilter-methods
madFilter<-,PreFilter,numeric-method	PreFilter-class
mas4	mas4
mas5	mas5
mas5.call	mas5.call
mboxplot	mboxplot-methods
mboxplot,ProcesSet-method	ProcesSet-class
mboxplot-methods	mboxplot-methods
metaProbesets	metaProbesets
mm	pm-methods
mm,DataTreeSet-method	DataTreeSet-class
mm-methods	pm-methods
mvaplot	mvaplot-methods
mvaplot,ExprTreeSet-method	ExprTreeSet-class
mvaplot-methods	mvaplot-methods
mvaplot.dev	mvaplot.dev
ncols	SchemeTreeSet-class
ncols,DataTreeSet-method	DataTreeSet-class
ncols,SchemeTreeSet-method	SchemeTreeSet-class
normalize	normalize
normalize.constant	normalize
normalize.lowess	normalize
normalize.quantiles	normalize
normalize.supsmu	normalize
normType	ExprTreeSet-class
normType,ExprTreeSet-method	ExprTreeSet-class
normType<-	ExprTreeSet-class
normType<-,ExprTreeSet,character-method	ExprTreeSet-class
nrows	SchemeTreeSet-class
nrows,DataTreeSet-method	DataTreeSet-class
nrows,SchemeTreeSet-method	SchemeTreeSet-class
numberFilters	Filter-class
numberFilters,Filter-method	Filter-class
pm	pm-methods
pm,DataTreeSet-method	DataTreeSet-class
pm-methods	pm-methods
pmplot	pmplot-methods
pmplot,DataTreeSet-method	DataTreeSet-class
pmplot-methods	pmplot-methods
PreFilter	PreFilter-constructor
prefilter	prefilter
PreFilter-class	PreFilter-class
presCall	presCall-methods
presCall,CallTreeSet-method	CallTreeSet-class
presCall-methods	presCall-methods
presCall<-	presCall-methods
presCall<-,CallTreeSet,data.frame-method	CallTreeSet-class
primcellInfo	ProjectInfo-class
primcellInfo,ProjectInfo-method	ProjectInfo-class
primcellInfo<-	ProjectInfo-class
primcellInfo<-,ProjectInfo,character-method	ProjectInfo-class
probeInfo	SchemeTreeSet-class
probeInfo,SchemeTreeSet-method	SchemeTreeSet-class
ProcesSet	ProcesSet-class
ProcesSet-class	ProcesSet-class
ProjectInfo	ProjectInfo-constructor
projectInfo	ProjectInfo-class
projectInfo,DataTreeSet-method	DataTreeSet-class
projectInfo,ProjectInfo-method	ProjectInfo-class
ProjectInfo-class	ProjectInfo-class
projectInfo<-	ProjectInfo-class
projectInfo<-,DataTreeSet,ProjectInfo-method	DataTreeSet-class
projectInfo<-,ProjectInfo,character-method	ProjectInfo-class
pvalData	presCall-methods
pvalData,CallTreeSet-method	CallTreeSet-class
pvalData-methods	presCall-methods
pvalData<-	presCall-methods
pvalData<-,CallTreeSet,data.frame-method	CallTreeSet-class
quantileFilter	quantileFilter-methods
quantileFilter,PreFilter-method	PreFilter-class
quantileFilter-methods	quantileFilter-methods
quantileFilter<-	quantileFilter-methods
quantileFilter<-,PreFilter,numeric-method	PreFilter-class
ratioFilter	ratioFilter-methods
ratioFilter,PreFilter-method	PreFilter-class
ratioFilter-methods	ratioFilter-methods
ratioFilter<-	ratioFilter-methods
ratioFilter<-,PreFilter,numeric-method	PreFilter-class
rawCELName	rawCELName-methods
rawCELName,DataTreeSet-method	DataTreeSet-class
rawCELName-methods	rawCELName-methods
removeBgrd	attachBgrd-methods
removeBgrd,DataTreeSet-method	DataTreeSet-class
removeBgrd-methods	attachBgrd-methods
removeCall	attachCall-methods
removeCall,CallTreeSet-method	CallTreeSet-class
removeCall-methods	attachCall-methods
removeExpr	attachExpr-methods
removeExpr,ExprTreeSet-method	ExprTreeSet-class
removeExpr-methods	attachExpr-methods
removeInten	attachInten-methods
removeInten,DataTreeSet-method	DataTreeSet-class
removeInten-methods	attachInten-methods
removeMask	attachMask-methods
removeMask,DataTreeSet-method	DataTreeSet-class
removeMask,SchemeTreeSet-method	SchemeTreeSet-class
removeMask-methods	attachMask-methods
removePVal	attachCall-methods
removePVal,CallTreeSet-method	CallTreeSet-class
removePVal-methods	attachCall-methods
rma	rma
ROOT	ROOT
root.browser	root.browser-methods
root.browser,TreeSet-method	TreeSet-class
root.call	root.call
root.data	root.data
root.density	root.density
root.expr	root.expr
root.graph1D	root.graph1D
root.graph2D	root.graph2D
root.hist1D	root.hist1D
root.hist2D	root.hist2D
root.hist3D	root.hist3D
root.image	root.image
root.mvaplot	root.mvaplot
root.profile	root.profile
root.scheme	root.scheme
rootFile	TreeSet-class
rootFile,TreeSet-method	TreeSet-class
rootFile<-	TreeSet-class
rootFile<-,TreeSet,character-method	TreeSet-class
sampleInfo	ProjectInfo-class
sampleInfo,ProjectInfo-method	ProjectInfo-class
sampleInfo<-	ProjectInfo-class
sampleInfo<-,ProjectInfo,character-method	ProjectInfo-class
schemeFile	ProcesSet-class
schemeFile,ProcesSet-method	ProcesSet-class
schemeFile<-	ProcesSet-class
schemeFile<-,ProcesSet,character-method	ProcesSet-class
schemeSet	ProcesSet-class
schemeSet,ProcesSet-method	ProcesSet-class
schemeSet<-	ProcesSet-class
schemeSet<-,ProcesSet,SchemeTreeSet-method	ProcesSet-class
SchemeTreeSet	SchemeTreeSet-class
SchemeTreeSet-class	SchemeTreeSet-class
se.exprs	ExprTreeSet-class
se.exprs,ExprTreeSet-method	ExprTreeSet-class
setName	TreeSet-class
setName,TreeSet-method	TreeSet-class
setName<-	TreeSet-class
setName<-,TreeSet,character-method	TreeSet-class
setType	TreeSet-class
setType,TreeSet-method	TreeSet-class
setType<-	TreeSet-class
setType<-,TreeSet,character-method	TreeSet-class
show,ProjectInfo-method	ProjectInfo-class
sourceInfo	ProjectInfo-class
sourceInfo,ProjectInfo-method	ProjectInfo-class
sourceInfo<-	ProjectInfo-class
sourceInfo<-,ProjectInfo,character-method	ProjectInfo-class
summarize	summarize
summarize.mas4	summarize
summarize.mas5	summarize
summarize.rma	summarize
tissueInfo	ProjectInfo-class
tissueInfo,ProjectInfo-method	ProjectInfo-class
tissueInfo<-	ProjectInfo-class
tissueInfo<-,ProjectInfo,character-method	ProjectInfo-class
treatmentInfo	ProjectInfo-class
treatmentInfo,ProjectInfo-method	ProjectInfo-class
treatmentInfo<-	ProjectInfo-class
treatmentInfo<-,ProjectInfo,character-method	ProjectInfo-class
treeNames	TreeSet-class
treeNames,TreeSet-method	TreeSet-class
TreeSet	TreeSet-class
TreeSet-class	TreeSet-class
type2Exten	type2Exten
UniFilter	UniFilter-constructor
unifilter	unifilter
UniFilter-class	UniFilter-class
uniTest	uniTest-methods
uniTest,UniFilter-method	UniFilter-class
uniTest-methods	uniTest-methods
uniTest<-	uniTest-methods
uniTest<-,UniFilter,character-method	UniFilter-class
unitestFilter	unitestFilter-methods
unitestFilter,UniFilter-method	UniFilter-class
unitestFilter-methods	unitestFilter-methods
unitestFilter<-	unitestFilter-methods
unitestFilter<-,UniFilter,character-method	UniFilter-class
validBgrd	DataTreeSet-class
validBgrd,DataTreeSet-method	DataTreeSet-class
validCall	CallTreeSet-class
validCall,CallTreeSet-method	CallTreeSet-class
validData	validData-methods
validData,AnalysisTreeSet-method	AnalysisTreeSet-class
validData,DataTreeSet-method	DataTreeSet-class
validData,FilterTreeSet-method	FilterTreeSet-class
validData,ProcesSet-method	ProcesSet-class
validFilter	AnalysisTreeSet-class
validFilter,AnalysisTreeSet-method	AnalysisTreeSet-class
validTreetype	validTreetype
varFilter	varFilter-methods
varFilter,PreFilter-method	PreFilter-class
varFilter-methods	varFilter-methods
varFilter<-	varFilter-methods
varFilter<-,PreFilter,numeric-method	PreFilter-class
volcanoplot	volcanoplot-methods
volcanoplot,AnalysisTreeSet-method	AnalysisTreeSet-class
volcanoplot-methods	volcanoplot-methods
xps	xps-package
xpsBgCorrect	bgcorrect
xpsBgCorrect,DataTreeSet-method	DataTreeSet-class
xpsBgCorrect-methods	bgcorrect
xpsDABGCall	dabg.call
xpsDABGCall,DataTreeSet-method	DataTreeSet-class
xpsDABGCall-methods	dabg.call
xpsINICall	ini.call
xpsINICall,DataTreeSet-method	DataTreeSet-class
xpsINICall-methods	ini.call
xpsMAS4	mas4
xpsMAS4,DataTreeSet-method	DataTreeSet-class
xpsMAS4-methods	mas4
xpsMAS5	mas5
xpsMAS5,DataTreeSet-method	DataTreeSet-class
xpsMAS5-methods	mas5
xpsMAS5Call	mas5.call
xpsMAS5Call,DataTreeSet-method	DataTreeSet-class
xpsMAS5Call-methods	mas5.call
xpsNormalize	normalize
xpsNormalize,DataTreeSet-method	DataTreeSet-class
xpsNormalize,ExprTreeSet-method	ExprTreeSet-class
xpsNormalize-methods	normalize
xpsOptions	xpsOptions
xpsPreFilter	prefilter
xpsPreFilter,ExprTreeSet-method	ExprTreeSet-class
xpsPreFilter-methods	prefilter
xpsPreprocess	express
xpsPreprocess,DataTreeSet-method	DataTreeSet-class
xpsPreprocess-methods	express
xpsRMA	rma
xpsRMA,DataTreeSet-method	DataTreeSet-class
xpsRMA-methods	rma
xpsSummarize	summarize
xpsSummarize,DataTreeSet-method	DataTreeSet-class
xpsSummarize-methods	summarize
xpsUniFilter	unifilter
xpsUniFilter,ExprTreeSet-method	ExprTreeSet-class
xpsUniFilter-methods	unifilter
