Entry: Aggregate
Aliases: Aggregate
Keywords: programming methods
Description: A Simple Aggregation Mechanism.
URL: ../../../library/Biobase/html/Aggregate.html

Entry: Biobase-package
Aliases: Biobase-package Biobase
Keywords: package
Description: Biobase Package Overview
URL: ../../../library/Biobase/html/Biobase-package.html

Entry: abstract
Aliases: abstract pubMedIds pubMedIds<- experimentData experimentData<-
Keywords: manip
Description: Retrieve feature and sample names from eSets and exprSets.
URL: ../../../library/Biobase/html/abstract.html

Entry: addVigs2WinMenu
Aliases: addVigs2WinMenu
Keywords: interface
Description: Add Menu Items to an Existing/New Menu of Window
URL: ../../../library/Biobase/html/addVig2Menu.html

Entry: annotatedDataFrameFrom-methods
Aliases: annotatedDataFrameFrom annotatedDataFrameFrom,AssayData-method
Keywords: methods
Description: Methods for Function annotatedDataFrameFrom in Package 'Biobase'
URL: ../../../library/Biobase/html/annotatedDataFrameFrom-methods.html

Entry: annotation
Aliases: annotation annotation<-
Keywords: manip
Description: Annotate eSet data.
URL: ../../../library/Biobase/html/annotation.html

Entry: assayData
Aliases: assayData assayData<-
Keywords: manip
Description: Retrieve assay data from eSets and exprSets.
URL: ../../../library/Biobase/html/assayData.html

Entry: biocReposList
Aliases: biocReposList
Keywords: utilities
Description: Return a list of Bioconductor package repositories
URL: ../../../library/Biobase/html/biocReposList.html

Entry: cache
Aliases: cache
Keywords: manip array
Description: Evaluate an expression if its value is not already cached.
URL: ../../../library/Biobase/html/cache.html

Entry: AnnotatedDataFrame
Aliases: class:AnnotatedDataFrame AnnotatedDataFrame AnnotatedDataFrame-class dimLabels [,AnnotatedDataFrame-method [[<-,AnnotatedDataFrame-method [[,AnnotatedDataFrame-method $<-,AnnotatedDataFrame-method $,AnnotatedDataFrame-method combine,AnnotatedDataFrame,AnnotatedDataFrame-method initialize,AnnotatedDataFrame-method coerce,phenoData,AnnotatedDataFrame-method dim,AnnotatedDataFrame-method dimLabels,AnnotatedDataFrame-method ncol,AnnotatedDataFrame-method pData<-,AnnotatedDataFrame,data.frame-method pData,AnnotatedDataFrame-method varMetadata<-,AnnotatedDataFrame,data.frame-method varMetadata,AnnotatedDataFrame-method sampleNames<-,AnnotatedDataFrame-method sampleNames,AnnotatedDataFrame-method featureNames,AnnotatedDataFrame-method featureNames<-,AnnotatedDataFrame-method show,AnnotatedDataFrame-method updateObject,AnnotatedDataFrame-method varLabels<-,AnnotatedDataFrame-method varLabels,AnnotatedDataFrame-method
Keywords: classes
Description: Class to Contain Measured Variables and Their Meta-Data Description.
URL: ../../../library/Biobase/html/class.AnnotatedDataFrame.html

Entry: AssayData-class
Aliases: AssayData-class AssayData combine,AssayData,AssayData-method featureNames,AssayData-method featureNames<-,AssayData-method sampleNames,AssayData-method sampleNames<-,AssayData-method storageMode,AssayData-method storageMode<-,AssayData,character-method assayDataNew assayDataValidMembers
Keywords: classes
Description: Class "AssayData"
URL: ../../../library/Biobase/html/class.AssayData.html

Entry: ExpressionSet
Aliases: class:ExpressionSet ExpressionSet ExpressionSet-class exprs,ExpressionSet-method exprs<-,ExpressionSet,matrix-method geneNames,ExpressionSet-method geneNames<-,ExpressionSet,character-method initialize,ExpressionSet-method coerce,exprSet,ExpressionSet-method coerce,eSet,ExpressionSet-method coerce,ExpressionSet,data.frame-method updateObject,ExpressionSet-method as.data.frame.ExpressionSet
Keywords: classes
Description: Class to Contain and Describe High-Throughput Expression Level Assays.
URL: ../../../library/Biobase/html/class.ExpressionSet.html

Entry: MIAME
Aliases: class:MIAME MIAME MIAME-class abstract,MIAME-method combine,MIAME,MIAME-method expinfo,MIAME-method hybridizations,MIAME-method normControls,MIAME-method otherInfo,MIAME-method preproc,MIAME-method notes,MIAME-method notes<-,MIAME,list-method pubMedIds,MIAME-method pubMedIds<-,MIAME,ANY-method samples,MIAME-method show,MIAME-method updateObject,MIAME-method isCurrent,MIAME,missing-method samples
Keywords: classes
Description: Class for Storing Microarray Experiment Information
URL: ../../../library/Biobase/html/class.MIAME.html

Entry: MultiSet
Aliases: class:MultiSet MultiSet MultiSet-class initialize,MultiSet-method coerce,eSet,MultiSet-method
Keywords: classes
Description: Class to Contain and Describe High-Throughput Expression Level Assays.
URL: ../../../library/Biobase/html/class.MultiSet.html

Entry: SnpSet
Aliases: class:SnpSet SnpSet SnpSet-class exprs<-,SnpSet,matrix-method exprs,SnpSet-method initialize,SnpSet-method
Keywords: classes
Description: Class to Contain Objects Describing High-Throughput SNP Assays.
URL: ../../../library/Biobase/html/class.SnpSet.html

Entry: Versioned
Aliases: Versioned-class Versioned initialize,Versioned-method isVersioned,Versioned-method classVersion,Versioned-method classVersion<-,Versioned,Versions-method isCurrent,Versioned,missing-method isCurrent,Versioned,character-method show,Versioned-method
Keywords: classes
Description: Class "Versioned"
URL: ../../../library/Biobase/html/class.Versioned.html

Entry: VersionedBiobase
Aliases: VersionedBiobase-class VersionedBiobase
Keywords: classes
Description: Class "VersionedBiobase"
URL: ../../../library/Biobase/html/class.VersionedBiobase.html

Entry: Versions
Aliases: Versions-class Versions initialize,Versions-method [,Versions-method [<-,Versions-method [[<-,Versions-method $<-,Versions-method Compare,Versions,Versions-method Compare,Versions,character-method Compare,character,Versions-method updateObject,Versions-method show,Versions-method coerce,Versions,character-method
Keywords: classes
Description: Class "Versions"
URL: ../../../library/Biobase/html/class.Versions.html

Entry: VersionsNull
Aliases: VersionsNull-class VersionsNull initialize,VersionsNull-method show,VersionsNull-method
Keywords: classes
Description: Class "VersionsNull"
URL: ../../../library/Biobase/html/class.VersionsNull.html

Entry: aggregator
Aliases: class:aggregator aggregator aggregator-class aggenv,aggregator-method aggfun,aggregator-method initfun,aggregator-method
Keywords: methods classes
Description: A Simple Class for Aggregators
URL: ../../../library/Biobase/html/class.aggregator.html

Entry: annotatedDataset
Aliases: class:annotatedDataset annotatedDataset annotatedDataset-class [[<-,annotatedDataset-method [[,annotatedDataset-method $<-,annotatedDataset-method $,annotatedDataset-method pData<-,annotatedDataset,ANY-method pData,annotatedDataset-method phenoData,annotatedDataset-method reporterInfo,annotatedDataset-method reporterInfo<-,annotatedDataset,data.frame-method varLabels,annotatedDataset-method
Keywords: classes
Description: Virtual Superset for 'exprSet', 'eSet' etc.
URL: ../../../library/Biobase/html/class.annotatedDataset.html

Entry: class:characterORMIAME
Aliases: class:characterORMIAME characterORMIAME-class
Keywords: classes
Description: Class to Make Older Versions Compatible
URL: ../../../library/Biobase/html/class.characterORmiame.html

Entry: container
Aliases: class:container container container-class [,container-method [[<-,container-method [[,container-method content,container-method length,container-method locked,container-method show,container-method
Keywords: methods classes
Description: A Lockable List Structure with Constraints on Content
URL: ../../../library/Biobase/html/class.container.html

Entry: eSet
Aliases: class:eSet eSet eSet-class [,eSet-method $,eSet-method $<-,eSet-method [[,eSet-method [[<-,eSet-method abstract,eSet-method annotation,eSet-method annotation<-,eSet,character-method assayData,eSet-method assayData<-,eSet,AssayData-method assayDataElement assayDataElementNames assayDataElementReplace coerce,exprSet,eSet-method combine,eSet,ANY-method combine,eSet,eSet-method description,eSet-method description<-,eSet,MIAME-method dim,eSet-method dims,eSet-method experimentData,eSet-method experimentData<-,eSet,MIAME-method exprs,eSet-method exprs<-,eSet,AssayData-method featureData featureData,eSet-method featureData<- featureData<-,eSet,AnnotatedDataFrame-method featureNames,eSet-method featureNames<-,eSet-method initialize,eSet-method getExpData,eSet,character-method ncol,eSet-method notes,eSet-method notes<-,eSet,list-method pData,eSet-method pData<-,eSet,data.frame-method phenoData,eSet-method phenoData<-,eSet,AnnotatedDataFrame-method pubMedIds,eSet-method pubMedIds<-,eSet,character-method reporterNames,eSet-method sampleNames,eSet-method sampleNames<-,eSet-method show,eSet-method storageMode,eSet-method storageMode<-,eSet,character-method varLabels,eSet-method varLabels<-,eSet-method varMetadata,eSet-method varMetadata<-,eSet,data.frame-method storageMode,eSet-method storageMode<-,eSet,character-method updateObject,eSet-method updateObjectTo,eSet,eSet-method listOrEnv SW SWPD swrep golubMergeSub
Keywords: classes
Description: Class to Contain High-Throughput Assays and Experimental Metadata
URL: ../../../library/Biobase/html/class.eSet.html

Entry: class:exprList
Aliases: class:exprList
Keywords: classes
Description: Class Union of a List and an Environment
URL: ../../../library/Biobase/html/class.exprList.html

Entry: class:exprMatrix
Aliases: class:exprMatrix exprMatrix-class
Keywords: classes
Description: Class Union for Objects Behaving Like a Matrix
URL: ../../../library/Biobase/html/class.exprMatrix.html

Entry: exprSet
Aliases: class:exprSet exprSet exprSet-class abstract,exprSet-method annotation<-,exprSet,ANY-method annotation,exprSet-method as.data.frame.exprSet,exprSet-method assayData,exprSet-method [,exprSet-method description<-,exprSet,ANY-method description,exprSet-method exprs2excel,exprSet-method exprs<-,exprSet,ANY-method exprs,exprSet-method geneNames<-,exprSet,ANY-method geneNames,exprSet-method featureNames<-,exprSet-method featureNames,exprSet-method iter,exprSet,missing,function-method iter,exprSet,missing,list-method iter,exprSet,character,function-method notes<-,exprSet,ANY-method notes,exprSet-method sampleNames<-,exprSet-method sampleNames,exprSet-method se.exprs<-,exprSet-method se.exprs,exprSet-method show,exprSet-method split,exprSet,factor,missing-method split,exprSet,vector,missing-method update2MIAME,exprSet-method updateObject,exprSet-method write.exprs,exprSet-method as.data.frame.exprSet split write.exprs update2MIAME exprs2excel
Keywords: methods classes
Description: Class for Microarray Data and Methods for Processing Them
URL: ../../../library/Biobase/html/class.exprSet.html

Entry: phenoData
Aliases: class:phenoData phenoData-class [,phenoData-method [[<-,phenoData-method [[,phenoData-method $<-,phenoData-method $,phenoData-method coerce,data.frame,phenoData-method combine,phenoData,phenoData-method combine,phenoData,ANY-method convertVarLabels,phenoData-method getVarMetadata getVarMetadata<- getVarMetadata,phenoData,character,character-method getVarMetadata,phenoData,character,missing-method pData<-,phenoData,ANY-method pData,phenoData-method phenoData<-,annotatedDataset,phenoData-method show,phenoData-method split,phenoData,vector,missing-method updateObject,phenoData-method varLabels,phenoData-method varMetadata,phenoData-method
Keywords: methods manip classes
Description: Class For Patient or Experiment Level Data
URL: ../../../library/Biobase/html/class.phenoData.html

Entry: classVersion
Aliases: classVersion classVersion<- classVersion,ANY-method classVersion,character-method
Keywords: manip
Description: Retrieve information about versioned classes
URL: ../../../library/Biobase/html/classVersion.html

Entry: combine
Aliases: combine combine,data.frame,data.frame-method
Keywords: manip
Description: Methods for Function combine in Package 'Biobase'
URL: ../../../library/Biobase/html/combine.html

Entry: contents
Aliases: contents
Keywords: manip
Description: Function to retrieve contents of environments
URL: ../../../library/Biobase/html/contents.html

Entry: copyEnv
Aliases: copyEnv l2e listLen
Keywords: utilities
Description: List-Environment interactions
URL: ../../../library/Biobase/html/copyEnv.html

Entry: copySubstitute
Aliases: copySubstitute
Keywords: connection programming
Description: Copy Between Connections or Files with Configure-Like Name-Value Substitution
URL: ../../../library/Biobase/html/copySubstitute.html

Entry: createPackage
Aliases: createPackage
Keywords: programming
Description: Create a Package Directory from a Template
URL: ../../../library/Biobase/html/createPackage.html

Entry: data:aaMap
Aliases: data:aaMap aaMap
Keywords: datasets
Description: Dataset: Names and Characteristics of Amino Acids
URL: ../../../library/Biobase/html/data.aaMap.html

Entry: data:eset
Aliases: data:eset eset
Keywords: datasets
Description: (Deprecated) dataset of class 'exprSet'
URL: ../../../library/Biobase/html/data.eset.html

Entry: data:geneData
Aliases: data:geneData geneData geneCovariate seD
Keywords: datasets
Description: A subset of some expression data.
URL: ../../../library/Biobase/html/data.geneData.html

Entry: reporter
Aliases: reporter
Keywords: datasets
Description: Example Data Frame Object for the ReporterInfo Slot
URL: ../../../library/Biobase/html/data.reporter.html

Entry: data:sample.ExpressionSet
Aliases: data:sample.ExpressionSet sample.ExpressionSet
Keywords: datasets
Description: Dataset of class 'ExpressionSet'
URL: ../../../library/Biobase/html/data.sample.ExpressionSet.html

Entry: data:sample.eSet
Aliases: data:sample.eSet sample.eSet
Keywords: datasets
Description: (Deprecated) dataset of class 'eSet'
URL: ../../../library/Biobase/html/data.sample.eSet.html

Entry: data:sample.exprSet.1
Aliases: data:sample.exprSet.1 sample.exprSet.1
Keywords: datasets
Description: Dataset of class 'exprSet'
URL: ../../../library/Biobase/html/data.sample.exprSet.1.html

Entry: data:sample.exprSet
Aliases: data:sample.exprSet sample.exprSet
Keywords: datasets
Description: Dataset of class 'exprSet'
URL: ../../../library/Biobase/html/data.sample.exprSet.html

Entry: Deprecated
Aliases: addVarMetadataEntry addVarMetadataEntry,phenoData,character,character-method getUnits getUnits,phenoData,character-method eList eList<- eList<-,eSet,AssayData-method eList,eSet-method eList<-,eSet,AssayData-method reporterNames
Keywords: internal
Description: Biobase Deprecated and Defunct
URL: ../../../library/Biobase/html/defunct.html

Entry: description
Aliases: description description<-
Keywords: manip
Description: Retrieve and set overall experimental information eSet-like classes.
URL: ../../../library/Biobase/html/description.html

Entry: dims
Aliases: dims
Keywords: manip
Description: Retrieve dimensions of all elements in a list or environment
URL: ../../../library/Biobase/html/dims.html

Entry: dumpPackTxt
Aliases: dumpPackTxt
Keywords: models
Description: Dump Textual Description of a Package
URL: ../../../library/Biobase/html/dumpPackTxt.html

Entry: esApply
Aliases: esApply
Keywords: models methods
Description: Apply for the Expression Data in 'exprSet'
URL: ../../../library/Biobase/html/esApply.html

Entry: exprs
Aliases: exprs exprs<- se.exprs se.exprs<-
Keywords: manip
Description: Retrieve expression data from eSets.
URL: ../../../library/Biobase/html/exprs.html

Entry: featureNames
Aliases: featureNames featureNames<- sampleNames sampleNames<- geneNames geneNames<-
Keywords: manip
Description: Retrieve feature and sample names from eSets and exprSets.
URL: ../../../library/Biobase/html/featureNames.html

Entry: getPkgVigs
Aliases: getPkgVigs
Keywords: utilities
Description: List Vignette Files for a Package
URL: ../../../library/Biobase/html/getPkgVigs.html

Entry: abstract
Aliases: aggenv aggfun content convertVarLabels df2pD expinfo getExpData hybridizations initfun iter locked normControls otherInfo preproc read.pD data.frameOrNULL-class listOrEnv-class bbsym geneCov contents,environment-method
Keywords: internal
Description: Internals
URL: ../../../library/Biobase/html/internals.html

Entry: isCurrent
Aliases: isCurrent isCurrent,ANY,ANY-method
Keywords: manip
Description: Use version information to test whether class is current
URL: ../../../library/Biobase/html/isCurrent.html

Entry: isUnique
Aliases: isUnique
Keywords: logic manip
Description: Determine Unique Elements
URL: ../../../library/Biobase/html/isUnique.html

Entry: isVersioned
Aliases: isVersioned isVersioned,ANY-method isVersioned,character-method
Keywords: manip
Description: Determine whether object or class contains versioning information
URL: ../../../library/Biobase/html/isVersioned.html

Entry: matchpt
Aliases: matchpt
Keywords: manip array
Description: Finds Nearest Neighbours for Sets of Points given by NxD Coordinates
URL: ../../../library/Biobase/html/matchpt.html

Entry: multiassign
Aliases: multiassign
Keywords: data
Description: Assign Values to a Names
URL: ../../../library/Biobase/html/multiassign.html

Entry: note
Aliases: note
Keywords: utilities
Description: Informational Messages
URL: ../../../library/Biobase/html/note.html

Entry: notes
Aliases: notes notes<-
Keywords: manip
Description: Retrieve and set eSet and exprSet notes.
URL: ../../../library/Biobase/html/notes.html

Entry: openPDF
Aliases: openPDF
Keywords: utilities
Description: Open PDF Files in a Standard Viewer
URL: ../../../library/Biobase/html/openPDF.html

Entry: openVignette
Aliases: openVignette
Keywords: utilities
Description: Open a Vignette or Show Vignette Selection Menu
URL: ../../../library/Biobase/html/openVignette.html

Entry: package.version
Aliases: package.version
Keywords: utilities
Description: Report Version of a Package
URL: ../../../library/Biobase/html/package.version.html

Entry: phenoData
Aliases: phenoData phenoData<- varLabels varLabels<- varMetadata varMetadata<- pData pData<-
Keywords: manip
Description: Retrieve information on experimental phenotypes recorded in eSet and exprSet-derived classes.
URL: ../../../library/Biobase/html/phenoData.html

Entry: read.MIAME
Aliases: read.MIAME
Keywords: file
Description: Read MIAME Information into an Instance of Class 'MIAME'
URL: ../../../library/Biobase/html/read.MIAME.html

Entry: read.exprSet
Aliases: read.exprSet
Keywords: file manip
Description: Read Experimental Data and into an 'exprSet' Object
URL: ../../../library/Biobase/html/read.exprSet.html

Entry: read.phenoData
Aliases: read.phenoData
Keywords: file manip
Description: Read 'phenoData'
URL: ../../../library/Biobase/html/read.phenoData.html

Entry: reporterInfo
Aliases: reporterInfo reporterInfo<-
Keywords: manip
Description: Retrieve and set information about reporters.
URL: ../../../library/Biobase/html/reporterInfo.html

Entry: reverseSplit
Aliases: reverseSplit
Keywords: manip
Description: A function to reverse the role of names and values in a list.
URL: ../../../library/Biobase/html/reverseSplit.html

Entry: rowQ
Aliases: rowQ rowQ,matrix,numeric-method rowQ,ExpressionSet,numeric-method rowQ,exprSet,numeric-method rowMin rowMax rowMedians rowMedians,matrix-method rowMedians,ExpressionSet-method rowMedians,exprSet-method
Keywords: manip
Description: A function to compute empirical row quantiles.
URL: ../../../library/Biobase/html/rowQ.html

Entry: selectSome
Aliases: selectSome
Keywords: models
Description: extract aspects of a vector for concise rendering
URL: ../../../library/Biobase/html/selectSome.html

Entry: storageMode
Aliases: storageMode storageMode<-
Keywords: manip
Description: Retrieve or set storage mode for eSets.
URL: ../../../library/Biobase/html/storageMode.html

Entry: strbreak
Aliases: strbreak
Keywords: character
Description: Break Character Strings to Fit Width
URL: ../../../library/Biobase/html/strbreak.html

Entry: testBioCConnection
Aliases: testBioCConnection
Keywords: utilities
Description: A function to check internet connectivity to Bioconductor
URL: ../../../library/Biobase/html/testBioCConnection.html

Entry: updateObject
Aliases: updateObject updateObjectTo updateObject,ANY-method updateObject,list-method updateObject,environment-method updateObjectTo,ANY,ANY-method updateObjectFromSlots getObjectSlots
Keywords: manip
Description: Update an object to its current class definition
URL: ../../../library/Biobase/html/updateObject.html

Entry: updateOldESet
Aliases: updateOldESet
Keywords: manip
Description: Update previously created eSet object to current eSet structure
URL: ../../../library/Biobase/html/updateOldESet.html

Entry: userQuery
Aliases: userQuery
Keywords: utilities
Description: A function to query the user for input
URL: ../../../library/Biobase/html/userQuery.html