Biobase-package	Biobase-package
$,AnnotatedDataFrame-method	class.AnnotatedDataFrame
$,eSet-method	class.eSet
$<-,AnnotatedDataFrame-method	class.AnnotatedDataFrame
$<-,eSet-method	class.eSet
$<-,Versions-method	class.Versions
aaMap	data.aaMap
abstract	abstract
abstract,eSet-method	class.eSet
abstract,MIAME-method	class.MIAME
addVigs2WinMenu	addVig2Menu
aggenv	internals
aggenv,aggregator-method	class.aggregator
aggfun	internals
aggfun,aggregator-method	class.aggregator
Aggregate	Aggregate
aggregator	class.aggregator
aggregator-class	class.aggregator
AnnotatedDataFrame	class.AnnotatedDataFrame
AnnotatedDataFrame-class	class.AnnotatedDataFrame
annotatedDataFrameFrom	annotatedDataFrameFrom-methods
annotatedDataFrameFrom,AssayData-method	annotatedDataFrameFrom-methods
annotatedDataFrameFrom,matrix-method	annotatedDataFrameFrom-methods
annotatedDataFrameFrom,NULL-method	annotatedDataFrameFrom-methods
annotatedDataset	defunct
annotatedDataset-class	defunct
annotation	annotation
annotation,eSet-method	class.eSet
annotation<-	annotation
annotation<-,eSet,character-method	class.eSet
anyMissing	anyMissing
as.data.frame.ExpressionSet	class.ExpressionSet
AssayData	class.AssayData
assayData	assayData
assayData,AssayData-method	class.AssayData
assayData,eSet-method	class.eSet
AssayData-class	class.AssayData
assayData<-	assayData
assayData<-,eSet,AssayData-method	class.eSet
assayDataElement	class.eSet
assayDataElement<-	class.eSet
assayDataElementNames	class.eSet
assayDataElementReplace	class.eSet
assayDataNew	class.AssayData
assayDataValidMembers	class.AssayData
Biobase	Biobase-package
biocReposList	biocReposList
cache	cache
channel	channel
channel,NChannelSet,character-method	class.NChannelSet
channelNames	channelNames
channelNames,NChannelSet-method	class.NChannelSet
characterORMIAME-class	class.characterORmiame
class.NChannelSet	class.NChannelSet
class:aggregator	class.aggregator
class:AnnotatedDataFrame	class.AnnotatedDataFrame
class:annotatedDataset	defunct
class:characterORMIAME	class.characterORmiame
class:container	class.container
class:eSet	class.eSet
class:ExpressionSet	class.ExpressionSet
class:exprList	defunct
class:exprMatrix	defunct
class:exprSet	defunct
class:MIAME	class.MIAME
class:MultiSet	class.MultiSet
class:phenoData	defunct
class:SnpSet	class.SnpSet
classVersion	classVersion
classVersion,ANY-method	classVersion
classVersion,character-method	classVersion
classVersion,Versioned-method	class.Versioned
classVersion<-	classVersion
classVersion<-,Versioned,Versions-method	class.Versioned
coerce,data.frame,AnnotatedDataFrame-method	class.AnnotatedDataFrame
coerce,eSet,ExpressionSet-method	class.ExpressionSet
coerce,eSet,MultiSet-method	class.MultiSet
coerce,ExpressionSet,data.frame-method	class.ExpressionSet
coerce,exprSet,ExpressionSet-method	class.ExpressionSet
coerce,phenoData,AnnotatedDataFrame-method	class.AnnotatedDataFrame
coerce,Versions,character-method	class.Versions
combine	combine
combine,AnnotatedDataFrame,AnnotatedDataFrame-method	class.AnnotatedDataFrame
combine,ANY,missing-method	combine
combine,AssayData,AssayData-method	class.AssayData
combine,data.frame,data.frame-method	combine
combine,eSet,ANY-method	class.eSet
combine,eSet,eSet-method	class.eSet
combine,matrix,matrix-method	combine
combine,MIAME,MIAME-method	class.MIAME
Compare,character,Versions-method	class.Versions
Compare,Versions,character-method	class.Versions
Compare,Versions,Versions-method	class.Versions
container	class.container
container-class	class.container
content	internals
content,container-method	class.container
contents	contents
contents,environment-method	internals
copyEnv	copyEnv
copySubstitute	copySubstitute
createPackage	createPackage
data.frameOrNULL-class	internals
data:aaMap	data.aaMap
data:geneCov	data.geneData
data:geneCovariate	data.geneData
data:geneData	data.geneData
data:reporter	data.reporter
data:sample.eSet	defunct
data:sample.ExpressionSet	data.sample.ExpressionSet
data:sample.exprSet	defunct
data:sample.exprSet.1	defunct
data:sample.MultiSet	data.sample.MultiSet
data:seD	data.geneData
description	description
description,eSet-method	class.eSet
description<-	description
description<-,eSet,MIAME-method	class.eSet
df2pD	defunct
dim,AnnotatedDataFrame-method	class.AnnotatedDataFrame
dim,eSet-method	class.eSet
dimLabels	class.AnnotatedDataFrame
dimLabels,AnnotatedDataFrame-method	class.AnnotatedDataFrame
dimLabels<-	class.AnnotatedDataFrame
dimLabels<-,AnnotatedDataFrame,character-method	class.AnnotatedDataFrame
dims	dims
dims,eSet-method	class.eSet
dumpPackTxt	dumpPackTxt
eList	defunct
eList,eSet-method	defunct
eList<-	defunct
eList<-,eSet,AssayData-method	defunct
esApply	esApply
esApply,ExpressionSet-method	class.ExpressionSet
eSet	class.eSet
eSet-class	class.eSet
experimentData	abstract
experimentData,eSet-method	class.eSet
experimentData<-	abstract
experimentData<-,eSet,MIAME-method	class.eSet
expinfo	internals
expinfo,MIAME-method	class.MIAME
ExpressionSet	class.ExpressionSet
ExpressionSet-class	class.ExpressionSet
exprList	defunct
exprList-class	defunct
exprMatrix	defunct
exprMatrix-class	defunct
exprs	exprs
exprs,eSet-method	class.eSet
exprs,ExpressionSet-method	class.ExpressionSet
exprs,SnpSet-method	class.SnpSet
exprs<-	exprs
exprs<-,eSet,AssayData-method	class.eSet
exprs<-,ExpressionSet,matrix-method	class.ExpressionSet
exprs<-,SnpSet,matrix-method	class.SnpSet
exprSet	defunct
exprSet-class	defunct
fData	featureData
fData,eSet-method	class.eSet
fData<-	featureData
fData<-,eSet,data.frame-method	class.eSet
featureData	featureData
featureData,eSet-method	class.eSet
featureData<-	featureData
featureData<-,eSet,AnnotatedDataFrame-method	class.eSet
featureNames	featureNames
featureNames,AnnotatedDataFrame-method	class.AnnotatedDataFrame
featureNames,AssayData-method	class.AssayData
featureNames,eSet-method	class.eSet
featureNames<-	featureNames
featureNames<-,AnnotatedDataFrame-method	class.AnnotatedDataFrame
featureNames<-,AssayData-method	class.AssayData
featureNames<-,eSet-method	class.eSet
fvarLabels	featureData
fvarLabels,eSet-method	class.eSet
fvarLabels<-	featureData
fvarLabels<-,eSet-method	class.eSet
fvarMetadata	featureData
fvarMetadata,eSet-method	class.eSet
fvarMetadata<-	featureData
fvarMetadata<-,eSet,data.frame-method	class.eSet
geneCov	data.geneData
geneCovariate	data.geneData
geneData	data.geneData
geneNames	defunct
geneNames,ExpressionSet-method	defunct
geneNames<-	defunct
geneNames<-,ExpressionSet,character-method	defunct
getExpData	defunct
getExpData,eSet,character-method	defunct
getObjectSlots	updateObject
getPkgVigs	getPkgVigs
hybridizations	internals
hybridizations,MIAME-method	class.MIAME
initfun	internals
initfun,aggregator-method	class.aggregator
initialize,aggregator-method	class.aggregator
initialize,AnnotatedDataFrame-method	class.AnnotatedDataFrame
initialize,annotatedDataset-method	defunct
initialize,eSet-method	class.eSet
initialize,ExpressionSet-method	class.ExpressionSet
initialize,exprSet-method	defunct
initialize,MultiSet-method	class.MultiSet
initialize,NChannelSet-method	class.NChannelSet
initialize,phenoData-method	defunct
initialize,SnpSet-method	class.SnpSet
initialize,Versioned-method	class.Versioned
initialize,Versions-method	class.Versions
initialize,VersionsNull-method	class.VersionsNull
isCurrent	isCurrent
isCurrent,ANY,ANY-method	isCurrent
isCurrent,MIAME,missing-method	class.MIAME
isCurrent,Versioned,character-method	class.Versioned
isCurrent,Versioned,missing-method	class.Versioned
isUnique	isUnique
isVersioned	isVersioned
isVersioned,ANY-method	isVersioned
isVersioned,character-method	isVersioned
isVersioned,Versioned-method	class.Versioned
l2e	copyEnv
lcPrefix	lcSuffix
lcPrefixC	lcSuffix
lcSuffix	lcSuffix
length,container-method	class.container
listLen	listLen
listOrEnv	class.eSet
listOrEnv-class	internals
locked	internals
locked,container-method	class.container
makeDataPackage	makeDataPackage
makeDataPackage,ANY-method	makeDataPackage
makeDataPackage,ExpressionSet-method	class.ExpressionSet
matchpt	matchpt
MIAME	class.MIAME
MIAME-class	class.MIAME
mkScalar	ScalarObject-class
multiassign	multiassign
MultiSet	class.MultiSet
MultiSet-class	class.MultiSet
NChannelSet	class.NChannelSet
NChannelSet-class	class.NChannelSet
ncol,AnnotatedDataFrame-method	class.AnnotatedDataFrame
ncol,eSet-method	class.eSet
normControls	internals
normControls,MIAME-method	class.MIAME
note	note
notes	notes
notes,eSet-method	class.eSet
notes,MIAME-method	class.MIAME
notes<-	notes
notes<-,eSet,ANY-method	class.eSet
notes<-,MIAME,character-method	class.MIAME
notes<-,MIAME,list-method	class.MIAME
openPDF	openPDF
openVignette	openVignette
otherInfo	internals
otherInfo,MIAME-method	class.MIAME
package.version	package.version
pData	phenoData
pData,AnnotatedDataFrame-method	class.AnnotatedDataFrame
pData,eSet-method	class.eSet
pData<-	phenoData
pData<-,AnnotatedDataFrame,data.frame-method	class.AnnotatedDataFrame
pData<-,eSet,data.frame-method	class.eSet
phenoData	phenoData
phenoData,eSet-method	class.eSet
phenoData-class	defunct
phenoData<-	phenoData
phenoData<-,eSet,AnnotatedDataFrame-method	class.eSet
preproc	class.MIAME
preproc,eSet-method	class.eSet
preproc,MIAME-method	class.MIAME
preproc<-	class.MIAME
preproc<-,eSet-method	class.eSet
preproc<-,MIAME-method	class.MIAME
pubMedIds	abstract
pubMedIds,eSet-method	class.eSet
pubMedIds,MIAME-method	class.MIAME
pubMedIds<-	abstract
pubMedIds<-,eSet,character-method	class.eSet
pubMedIds<-,MIAME,ANY-method	class.MIAME
read.AnnotatedDataFrame	read.AnnotatedDataFrame
read.exprSet	defunct
read.MIAME	read.MIAME
read.pD	defunct
read.phenoData	defunct
readExpressionSet	readExpressionSet
reporter	data.reporter
reporterNames	defunct
reporterNames,eSet-method	defunct
reporterNames<-	defunct
reporterNames<-,eSet,character-method	defunct
reverseSplit	reverseSplit
rowMax	rowQ
rowMedians	rowMedians
rowMedians,ExpressionSet-method	rowMedians
rowMedians,matrix-method	rowMedians
rowMin	rowQ
rowQ	rowQ
rowQ,ExpressionSet,numeric-method	rowQ
rowQ,matrix,numeric-method	rowQ
sample.eSet	defunct
sample.ExpressionSet	data.sample.ExpressionSet
sample.exprSet	defunct
sample.exprSet.1	defunct
sample.MultiSet	data.sample.MultiSet
sampleNames	featureNames
sampleNames,AnnotatedDataFrame-method	class.AnnotatedDataFrame
sampleNames,AssayData-method	class.AssayData
sampleNames,eSet-method	class.eSet
sampleNames,NChannelSet-method	class.NChannelSet
sampleNames<-	featureNames
sampleNames<-,AnnotatedDataFrame,ANY-method	class.AnnotatedDataFrame
sampleNames<-,AssayData,ANY-method	class.AssayData
sampleNames<-,AssayData,list-method	class.AssayData
sampleNames<-,eSet,ANY-method	class.eSet
sampleNames<-,NChannelSet,list-method	class.NChannelSet
samples	class.MIAME
samples,MIAME-method	class.MIAME
ScalarCharacter-class	ScalarObject-class
ScalarInteger-class	ScalarObject-class
ScalarNumeric-class	ScalarObject-class
ScalarObject-class	ScalarObject-class
se.exprs	exprs
se.exprs<-	exprs
seD	data.geneData
selectChannels	selectChannels
selectChannels,NChannelSet,character-method	class.NChannelSet
selectSome	selectSome
show,AnnotatedDataFrame-method	class.AnnotatedDataFrame
show,container-method	class.container
show,eSet-method	class.eSet
show,MIAME-method	class.MIAME
show,ScalarCharacter-method	ScalarObject-class
show,ScalarObject-method	ScalarObject-class
show,Versioned-method	class.Versioned
show,Versions-method	class.Versions
show,VersionsNull-method	class.VersionsNull
SnpSet	class.SnpSet
SnpSet-class	class.SnpSet
storageMode	storageMode
storageMode,AssayData-method	class.AssayData
storageMode,eSet-method	class.eSet
storageMode<-	storageMode
storageMode<-,AssayData,character-method	class.AssayData
storageMode<-,eSet,character-method	class.eSet
strbreak	strbreak
subListExtract	subListExtract
SW	class.eSet
testBioCConnection	testBioCConnection
updateObject	updateObject
updateObject,AnnotatedDataFrame-method	class.AnnotatedDataFrame
updateObject,ANY-method	updateObject
updateObject,environment-method	updateObject
updateObject,eSet-method	class.eSet
updateObject,ExpressionSet-method	class.ExpressionSet
updateObject,list-method	updateObject
updateObject,MIAME-method	class.MIAME
updateObject,Versions-method	class.Versions
updateObjectFromSlots	updateObject
updateObjectTo	updateObject
updateObjectTo,ANY,ANY-method	updateObject
updateObjectTo,eSet,eSet-method	class.eSet
updateOldESet	updateOldESet
updateOldMiame	defunct
userQuery	userQuery
validMsg	validMsg
varLabels	phenoData
varLabels,AnnotatedDataFrame-method	class.AnnotatedDataFrame
varLabels,eSet-method	class.eSet
varLabels<-	phenoData
varLabels<-,AnnotatedDataFrame-method	class.AnnotatedDataFrame
varLabels<-,eSet-method	class.eSet
varMetadata	phenoData
varMetadata,AnnotatedDataFrame-method	class.AnnotatedDataFrame
varMetadata,eSet-method	class.eSet
varMetadata<-	phenoData
varMetadata<-,AnnotatedDataFrame,data.frame-method	class.AnnotatedDataFrame
varMetadata<-,eSet,data.frame-method	class.eSet
Versioned	class.Versioned
Versioned-class	class.Versioned
VersionedBiobase	class.VersionedBiobase
VersionedBiobase-class	class.VersionedBiobase
Versions	class.Versions
Versions-class	class.Versions
VersionsNull	class.VersionsNull
VersionsNull-class	class.VersionsNull
write.exprs	class.ExpressionSet
write.exprs,ExpressionSet-method	class.ExpressionSet
[,AnnotatedDataFrame-method	class.AnnotatedDataFrame
[,container-method	class.container
[,eSet-method	class.eSet
[,Versions-method	class.Versions
[<-,Versions-method	class.Versions
[[,AnnotatedDataFrame-method	class.AnnotatedDataFrame
[[,container-method	class.container
[[,eSet-method	class.eSet
[[<-,AnnotatedDataFrame-method	class.AnnotatedDataFrame
[[<-,container-method	class.container
[[<-,eSet-method	class.eSet
[[<-,Versions-method	class.Versions
