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
extenPart	extenPart
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	intensity-methods
intensity,DataTreeSet-method	DataTreeSet-class
intensity-methods	intensity-methods
intensity<-	intensity-methods
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
namePart	namePart
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.merge.data	root.merge.data
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	validCall-methods
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
validExpr	validExpr-methods
validExpr,ExprTreeSet-method	ExprTreeSet-class
validFilter	AnalysisTreeSet-class
validFilter,AnalysisTreeSet-method	AnalysisTreeSet-class
validPVal	validCall-methods
validPVal,CallTreeSet-method	CallTreeSet-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
