Biobase-package	Biobase-package
$,AnnotatedDataFrame-method	class.AnnotatedDataFrame
$,annotatedDataset-method	class.annotatedDataset
$,eSet-method	class.eSet
$,phenoData-method	class.phenoData
$<-,AnnotatedDataFrame-method	class.AnnotatedDataFrame
$<-,annotatedDataset-method	class.annotatedDataset
$<-,eSet-method	class.eSet
$<-,phenoData-method	class.phenoData
$<-,Versions-method	class.Versions
aaMap	data.aaMap
abstract	abstract
abstract,eSet-method	class.eSet
abstract,exprSet-method	class.exprSet
abstract,MIAME-method	class.MIAME
addVarMetadataEntry	defunct
addVarMetadataEntry,phenoData,character,character-method	defunct
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
annotatedDataset	class.annotatedDataset
annotatedDataset-class	class.annotatedDataset
annotation	annotation
annotation,eSet-method	class.eSet
annotation,exprSet-method	class.exprSet
annotation<-	annotation
annotation<-,eSet,character-method	class.eSet
annotation<-,exprSet,ANY-method	class.exprSet
as.data.frame.ExpressionSet	class.ExpressionSet
as.data.frame.exprSet	class.exprSet
as.data.frame.exprSet,exprSet-method	class.exprSet
AssayData	class.AssayData
assayData	assayData
assayData,eSet-method	class.eSet
assayData,exprSet-method	class.exprSet
AssayData-class	class.AssayData
assayData<-	assayData
assayData<-,eSet,AssayData-method	class.eSet
assayDataElement	class.eSet
assayDataElementNames	class.eSet
assayDataElementReplace	class.eSet
assayDataNew	class.AssayData
assayDataValidMembers	class.AssayData
bbsym	internals
Biobase	Biobase-package
biocReposList	biocReposList
cache	cache
characterORMIAME-class	class.characterORmiame
class:aggregator	class.aggregator
class:AnnotatedDataFrame	class.AnnotatedDataFrame
class:annotatedDataset	class.annotatedDataset
class:characterORMIAME	class.characterORmiame
class:container	class.container
class:eSet	class.eSet
class:ExpressionSet	class.ExpressionSet
class:exprList	class.exprList
class:exprMatrix	class.exprMatrix
class:exprSet	class.exprSet
class:MIAME	class.MIAME
class:MultiSet	class.MultiSet
class:phenoData	class.phenoData
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,phenoData-method	class.phenoData
coerce,eSet,ExpressionSet-method	class.ExpressionSet
coerce,eSet,MultiSet-method	class.MultiSet
coerce,ExpressionSet,data.frame-method	class.ExpressionSet
coerce,exprSet,eSet-method	class.eSet
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,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,MIAME,MIAME-method	class.MIAME
combine,phenoData,ANY-method	class.phenoData
combine,phenoData,phenoData-method	class.phenoData
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
convertVarLabels	internals
convertVarLabels,phenoData-method	class.phenoData
copyEnv	copyEnv
copySubstitute	copySubstitute
createPackage	createPackage
data.frameOrNULL-class	internals
data:aaMap	data.aaMap
data:eset	data.eset
data:geneData	data.geneData
data:sample.eSet	data.sample.eSet
data:sample.ExpressionSet	data.sample.ExpressionSet
data:sample.exprSet	data.sample.exprSet
data:sample.exprSet.1	data.sample.exprSet.1
description	description
description,eSet-method	class.eSet
description,exprSet-method	class.exprSet
description<-	description
description<-,eSet,MIAME-method	class.eSet
description<-,exprSet,ANY-method	class.exprSet
df2pD	internals
dim,AnnotatedDataFrame-method	class.AnnotatedDataFrame
dim,eSet-method	class.eSet
dimLabels	class.AnnotatedDataFrame
dimLabels,AnnotatedDataFrame-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
eSet	class.eSet
eset	data.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
exprMatrix-class	class.exprMatrix
exprs	exprs
exprs,eSet-method	class.eSet
exprs,ExpressionSet-method	class.ExpressionSet
exprs,exprSet-method	class.exprSet
exprs,SnpSet-method	class.SnpSet
exprs2excel	class.exprSet
exprs2excel,exprSet-method	class.exprSet
exprs<-	exprs
exprs<-,eSet,AssayData-method	class.eSet
exprs<-,ExpressionSet,matrix-method	class.ExpressionSet
exprs<-,exprSet,ANY-method	class.exprSet
exprs<-,SnpSet,matrix-method	class.SnpSet
exprSet	class.exprSet
exprSet-class	class.exprSet
featureData	class.eSet
featureData,eSet-method	class.eSet
featureData<-	class.eSet
featureData<-,eSet,AnnotatedDataFrame-method	class.eSet
featureNames	featureNames
featureNames,AnnotatedDataFrame-method	class.AnnotatedDataFrame
featureNames,AssayData-method	class.AssayData
featureNames,eSet-method	class.eSet
featureNames,exprSet-method	class.exprSet
featureNames<-	featureNames
featureNames<-,AnnotatedDataFrame-method	class.AnnotatedDataFrame
featureNames<-,AssayData-method	class.AssayData
featureNames<-,eSet-method	class.eSet
featureNames<-,exprSet-method	class.exprSet
geneCov	internals
geneCovariate	data.geneData
geneData	data.geneData
geneNames	featureNames
geneNames,ExpressionSet-method	class.ExpressionSet
geneNames,exprSet-method	class.exprSet
geneNames<-	featureNames
geneNames<-,ExpressionSet,character-method	class.ExpressionSet
geneNames<-,exprSet,ANY-method	class.exprSet
getExpData	internals
getExpData,eSet,character-method	class.eSet
getObjectSlots	updateObject
getPkgVigs	getPkgVigs
getUnits	defunct
getUnits,phenoData,character-method	defunct
getVarMetadata	class.phenoData
getVarMetadata,phenoData,character,character-method	class.phenoData
getVarMetadata,phenoData,character,missing-method	class.phenoData
getVarMetadata<-	class.phenoData
golubMergeSub	class.eSet
hybridizations	internals
hybridizations,MIAME-method	class.MIAME
initfun	internals
initfun,aggregator-method	class.aggregator
initialize,AnnotatedDataFrame-method	class.AnnotatedDataFrame
initialize,eSet-method	class.eSet
initialize,ExpressionSet-method	class.ExpressionSet
initialize,MultiSet-method	class.MultiSet
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
iter	internals
iter,exprSet,character,function-method	class.exprSet
iter,exprSet,missing,function-method	class.exprSet
iter,exprSet,missing,list-method	class.exprSet
l2e	copyEnv
length,container-method	class.container
listLen	copyEnv
listOrEnv	class.eSet
listOrEnv-class	internals
locked	internals
locked,container-method	class.container
matchpt	matchpt
MIAME	class.MIAME
MIAME-class	class.MIAME
multiassign	multiassign
MultiSet	class.MultiSet
MultiSet-class	class.MultiSet
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,exprSet-method	class.exprSet
notes,MIAME-method	class.MIAME
notes<-	notes
notes<-,eSet,list-method	class.eSet
notes<-,exprSet,ANY-method	class.exprSet
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,annotatedDataset-method	class.annotatedDataset
pData,eSet-method	class.eSet
pData,phenoData-method	class.phenoData
pData<-	phenoData
pData<-,AnnotatedDataFrame,data.frame-method	class.AnnotatedDataFrame
pData<-,annotatedDataset,ANY-method	class.annotatedDataset
pData<-,eSet,data.frame-method	class.eSet
pData<-,phenoData,ANY-method	class.phenoData
phenoData	phenoData
phenoData,annotatedDataset-method	class.annotatedDataset
phenoData,eSet-method	class.eSet
phenoData-class	class.phenoData
phenoData<-	phenoData
phenoData<-,annotatedDataset,phenoData-method	class.phenoData
phenoData<-,eSet,AnnotatedDataFrame-method	class.eSet
preproc	internals
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.exprSet	read.exprSet
read.MIAME	read.MIAME
read.pD	internals
read.phenoData	read.phenoData
reporter	data.reporter
reporterInfo	reporterInfo
reporterInfo,annotatedDataset-method	class.annotatedDataset
reporterInfo<-	reporterInfo
reporterInfo<-,annotatedDataset,data.frame-method	class.annotatedDataset
reporterNames	defunct
reporterNames,eSet-method	class.eSet
reverseSplit	reverseSplit
rowMax	rowQ
rowMedians	rowQ
rowMedians,ExpressionSet-method	rowQ
rowMedians,exprSet-method	rowQ
rowMedians,matrix-method	rowQ
rowMin	rowQ
rowQ	rowQ
rowQ,ExpressionSet,numeric-method	rowQ
rowQ,exprSet,numeric-method	rowQ
rowQ,matrix,numeric-method	rowQ
sample.eSet	data.sample.eSet
sample.ExpressionSet	data.sample.ExpressionSet
sample.exprSet	data.sample.exprSet
sample.exprSet.1	data.sample.exprSet.1
sampleNames	featureNames
sampleNames,AnnotatedDataFrame-method	class.AnnotatedDataFrame
sampleNames,AssayData-method	class.AssayData
sampleNames,eSet-method	class.eSet
sampleNames,exprSet-method	class.exprSet
sampleNames<-	featureNames
sampleNames<-,AnnotatedDataFrame-method	class.AnnotatedDataFrame
sampleNames<-,AssayData-method	class.AssayData
sampleNames<-,eSet-method	class.eSet
sampleNames<-,exprSet-method	class.exprSet
samples	class.MIAME
samples,MIAME-method	class.MIAME
se.exprs	exprs
se.exprs,exprSet-method	class.exprSet
se.exprs<-	exprs
se.exprs<-,exprSet-method	class.exprSet
seD	data.geneData
selectSome	selectSome
show,AnnotatedDataFrame-method	class.AnnotatedDataFrame
show,container-method	class.container
show,eSet-method	class.eSet
show,exprSet-method	class.exprSet
show,MIAME-method	class.MIAME
show,phenoData-method	class.phenoData
show,Versioned-method	class.Versioned
show,Versions-method	class.Versions
show,VersionsNull-method	class.VersionsNull
SnpSet	class.SnpSet
SnpSet-class	class.SnpSet
split	class.exprSet
split,exprSet,factor,missing-method	class.exprSet
split,exprSet,vector,missing-method	class.exprSet
split,phenoData,vector,missing-method	class.phenoData
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
SW	class.eSet
SWPD	class.eSet
swrep	class.eSet
testBioCConnection	testBioCConnection
update2MIAME	class.exprSet
update2MIAME,exprSet-method	class.exprSet
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,exprSet-method	class.exprSet
updateObject,list-method	updateObject
updateObject,MIAME-method	class.MIAME
updateObject,phenoData-method	class.phenoData
updateObject,Versions-method	class.Versions
updateObjectFromSlots	updateObject
updateObjectTo	updateObject
updateObjectTo,ANY,ANY-method	updateObject
updateObjectTo,eSet,eSet-method	class.eSet
updateOldESet	updateOldESet
userQuery	userQuery
varLabels	phenoData
varLabels,AnnotatedDataFrame-method	class.AnnotatedDataFrame
varLabels,annotatedDataset-method	class.annotatedDataset
varLabels,eSet-method	class.eSet
varLabels,phenoData-method	class.phenoData
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-method	class.phenoData
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.exprSet
write.exprs,exprSet-method	class.exprSet
[,AnnotatedDataFrame-method	class.AnnotatedDataFrame
[,container-method	class.container
[,eSet-method	class.eSet
[,exprSet-method	class.exprSet
[,phenoData-method	class.phenoData
[,Versions-method	class.Versions
[<-,Versions-method	class.Versions
[[,AnnotatedDataFrame-method	class.AnnotatedDataFrame
[[,annotatedDataset-method	class.annotatedDataset
[[,container-method	class.container
[[,eSet-method	class.eSet
[[,phenoData-method	class.phenoData
[[<-,AnnotatedDataFrame-method	class.AnnotatedDataFrame
[[<-,annotatedDataset-method	class.annotatedDataset
[[<-,container-method	class.container
[[<-,eSet-method	class.eSet
[[<-,phenoData-method	class.phenoData
[[<-,Versions-method	class.Versions