# Biobase: Base functions for Bioconductor

## Documentation for package `Biobase' version 1.10.1

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A B C D E F G H I L M N O P R S T U V W misc

## -- --

Biobase-package | Biobase Package Overview

## -- --

$,AnnotatedDataFrame-method | Class to Contain Measured Variables and Their Meta-Data Description.
$,annotatedDataset-method | Virtual Superset for 'exprSet', 'eSet' etc.
$,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
$,phenoData-method | Class For Patient or Experiment Level Data
$<-,AnnotatedDataFrame-method | Class to Contain Measured Variables and Their Meta-Data Description.
$<-,annotatedDataset-method | Virtual Superset for 'exprSet', 'eSet' etc.
$<-,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
$<-,phenoData-method | Class For Patient or Experiment Level Data

## -- A --

aaMap | Dataset: Names and Characteristics of Amino Acids
abstract | Retrieve feature and sample names from eSets and exprSets.
abstract,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
abstract,exprSet-method | Class for Microarray Data and Methods for Processing Them
abstract,MIAME-method | Class for Storing Microarray Experiment Information
addVigs2WinMenu | Add Menu Items to an Existing/New Menu of Window
aggenv,aggregator-method | A Simple Class for Aggregators
aggfun,aggregator-method | A Simple Class for Aggregators
Aggregate | A Simple Aggregation Mechanism.
aggregator | A Simple Class for Aggregators
aggregator-class | A Simple Class for Aggregators
AnnotatedDataFrame | Class to Contain Measured Variables and Their Meta-Data Description.
AnnotatedDataFrame-class | Class to Contain Measured Variables and Their Meta-Data Description.
annotatedDataset | Virtual Superset for 'exprSet', 'eSet' etc.
annotatedDataset-class | Virtual Superset for 'exprSet', 'eSet' etc.
annotation | Annotate eSet data.
annotation,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
annotation,exprSet-method | Class for Microarray Data and Methods for Processing Them
annotation<-,eSet,character-method | Class to Contain High-Throughput Assays and Experimental Metadata
annotation<-,exprSet-method | Class for Microarray Data and Methods for Processing Them
as.data.frame.exprSet | Class for Microarray Data and Methods for Processing Them
as.data.frame.exprSet,exprSet-method | Class for Microarray Data and Methods for Processing Them
AssayData | Class "AssayData"
assayData | Retrieve assay data from eSets and exprSets.
assayData,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
assayData,exprSet-method | Class for Microarray Data and Methods for Processing Them
AssayData-class | Class "AssayData"
assayData<-,eSet,AssayData-method | Class to Contain High-Throughput Assays and Experimental Metadata
assayDataElement | Class "AssayData"
assayDataElementNames | Class "AssayData"
assayDataElementReplace | Class "AssayData"
assayDataNew | Class "AssayData"
assayDataValidMembers | Class "AssayData"

## -- B --

Biobase | Biobase Package Overview
biocReposList | Return a list of Bioconductor package repositories

## -- C --

cache | Evaluate an expression if its value is not already cached.
characterORMIAME-class | Class to Make Older Versions Compatible
class:aggregator | A Simple Class for Aggregators
class:AnnotatedDataFrame | Class to Contain Measured Variables and Their Meta-Data Description.
class:annotatedDataset | Virtual Superset for 'exprSet', 'eSet' etc.
class:characterORMIAME | Class to Make Older Versions Compatible
class:container | A Lockable List Structure with Constraints on Content
class:eSet | Class to Contain High-Throughput Assays and Experimental Metadata
class:ExpressionSet | Class to Contain and Describe High-Throughput Expression Level Assays.
class:exprList | Class Union of a List and an Environment
class:exprMatrix | Class Union for Objects Behaving Like a Matrix
class:exprSet | Class for Microarray Data and Methods for Processing Them
class:MIAME | Class for Storing Microarray Experiment Information
class:MultiSet | Class to Contain and Describe High-Throughput Expression Level Assays.
class:phenoData | Class For Patient or Experiment Level Data
class:SnpSet | Class to Contain Objects Describing High-Throughput SNP Assays.
coerce,data.frame,phenoData-method | Class For Patient or Experiment Level Data
coerce,exprSet,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
coerce,exprSet,ExpressionSet-method | Class to Contain and Describe High-Throughput Expression Level Assays.
coerce,phenoData,AnnotatedDataFrame-method | Class to Contain Measured Variables and Their Meta-Data Description.
combine | Combine Data Into a Single Object.
combine,AnnotatedDataFrame,AnnotatedDataFrame-method | Class to Contain Measured Variables and Their Meta-Data Description.
combine,AssayData,AssayData-method | Class "AssayData"
combine,eSet,ANY-method | Class to Contain High-Throughput Assays and Experimental Metadata
combine,eSet,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
combine,MIAME,MIAME-method | Class for Storing Microarray Experiment Information
combine,phenoData,ANY-method | Class For Patient or Experiment Level Data
combine,phenoData,phenoData-method | Class For Patient or Experiment Level Data
container | A Lockable List Structure with Constraints on Content
container-class | A Lockable List Structure with Constraints on Content
content,container-method | A Lockable List Structure with Constraints on Content
contents | Function to retrieve contents of environments
convertVarLabels,phenoData-method | Class For Patient or Experiment Level Data
copyEnv | List-Environment interactions
copySubstitute | Copy Between Connections or Files with Configure-Like Name-Value Substitution
createPackage | Create a Package Directory from a Template

## -- D --

data:aaMap | Dataset: Names and Characteristics of Amino Acids
data:eset | (Deprecated) dataset of class 'exprSet'
data:geneData | A subset of some expression data.
data:sample.eSet | Dataset of class 'eSet'
data:sample.ExpressionSet | Dataset of class 'ExpressionSet'
data:sample.exprSet | Dataset of class 'exprSet'
data:sample.exprSet.1 | Dataset of class 'exprSet'
description | Retrieve and set overall experimental information eSet-like classes.
description,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
description,exprSet-method | Class for Microarray Data and Methods for Processing Them
description<-,eSet,MIAME-method | Class to Contain High-Throughput Assays and Experimental Metadata
description<-,exprSet-method | Class for Microarray Data and Methods for Processing Them
dim,AnnotatedDataFrame-method | Class to Contain Measured Variables and Their Meta-Data Description.
dim,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
dims | Retrieve dimensions of all elements in a list or environment
dims,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
dumpPackTxt | Dump Textual Description of a Package

## -- E --

esApply | Apply for the Expression Data in 'exprSet'
eSet | Class to Contain High-Throughput Assays and Experimental Metadata
eset | (Deprecated) dataset of class 'exprSet'
eSet-class | Class to Contain High-Throughput Assays and Experimental Metadata
experimentData | Retrieve feature and sample names from eSets and exprSets.
experimentData,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
experimentData<-,eSet,MIAME-method | Class to Contain High-Throughput Assays and Experimental Metadata
expinfo,MIAME-method | Class for Storing Microarray Experiment Information
ExpressionSet | Class to Contain and Describe High-Throughput Expression Level Assays.
ExpressionSet-class | Class to Contain and Describe High-Throughput Expression Level Assays.
exprMatrix-class | Class Union for Objects Behaving Like a Matrix
exprs | Retrieve expression data from eSets.
exprs,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
exprs,ExpressionSet-method | Class to Contain and Describe High-Throughput Expression Level Assays.
exprs,exprSet-method | Class for Microarray Data and Methods for Processing Them
exprs,SnpSet-method | Class to Contain Objects Describing High-Throughput SNP Assays.
exprs2excel | Class for Microarray Data and Methods for Processing Them
exprs2excel,exprSet-method | Class for Microarray Data and Methods for Processing Them
exprs<-,eSet,AssayData-method | Class to Contain High-Throughput Assays and Experimental Metadata
exprs<-,ExpressionSet,matrix-method | Class to Contain and Describe High-Throughput Expression Level Assays.
exprs<-,exprSet-method | Class for Microarray Data and Methods for Processing Them
exprs<-,SnpSet,matrix-method | Class to Contain Objects Describing High-Throughput SNP Assays.
exprSet | Class for Microarray Data and Methods for Processing Them
exprSet-class | Class for Microarray Data and Methods for Processing Them

## -- F --

featureNames | Retrieve feature and sample names from eSets and exprSets.
featureNames,AssayData-method | Class "AssayData"
featureNames,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
featureNames<-,AssayData-method | Class "AssayData"
featureNames<-,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata

## -- G --

geneCovariate | A subset of some expression data.
geneData | A subset of some expression data.
geneNames | Retrieve feature and sample names from eSets and exprSets.
geneNames,exprSet-method | Class for Microarray Data and Methods for Processing Them
geneNames<-,exprSet-method | Class for Microarray Data and Methods for Processing Them
getExpData,eSet,character-method | Class to Contain High-Throughput Assays and Experimental Metadata
getPkgVigs | List Vignette Files for a Package
getVarMetadata | Class For Patient or Experiment Level Data
getVarMetadata,phenoData,character,character-method | Class For Patient or Experiment Level Data
getVarMetadata,phenoData,character,missing-method | Class For Patient or Experiment Level Data
golubMergeSub | Class to Contain High-Throughput Assays and Experimental Metadata

## -- H --

hybridizations,MIAME-method | Class for Storing Microarray Experiment Information

## -- I --

initfun,aggregator-method | A Simple Class for Aggregators
initialize,AnnotatedDataFrame-method | Class to Contain Measured Variables and Their Meta-Data Description.
initialize,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
initialize,ExpressionSet-method | Class to Contain and Describe High-Throughput Expression Level Assays.
initialize,MultiSet-method | Class to Contain and Describe High-Throughput Expression Level Assays.
initialize,SnpSet-method | Class to Contain Objects Describing High-Throughput SNP Assays.
isUnique | Determine Unique Elements
iter,exprSet,character,function-method | Class for Microarray Data and Methods for Processing Them
iter,exprSet,missing,function-method | Class for Microarray Data and Methods for Processing Them
iter,exprSet,missing,list-method | Class for Microarray Data and Methods for Processing Them

## -- L --

l2e | List-Environment interactions
length,container-method | A Lockable List Structure with Constraints on Content
listLen | List-Environment interactions
listOrEnv | Class to Contain High-Throughput Assays and Experimental Metadata
locked,container-method | A Lockable List Structure with Constraints on Content

## -- M --

matchpt | Finds Nearest Neighbours for Sets of Points given by NxD Coordinates
MIAME | Class for Storing Microarray Experiment Information
MIAME-class | Class for Storing Microarray Experiment Information
multiassign | Assign Values to a Names
MultiSet | Class to Contain and Describe High-Throughput Expression Level Assays.
MultiSet-class | Class to Contain and Describe High-Throughput Expression Level Assays.

## -- N --

ncol,AnnotatedDataFrame-method | Class to Contain Measured Variables and Their Meta-Data Description.
ncol,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
normControls,MIAME-method | Class for Storing Microarray Experiment Information
note | Informational Messages
notes | Retrieve and set eSet and exprSet notes.
notes,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
notes,exprSet-method | Class for Microarray Data and Methods for Processing Them
notes,MIAME-method | Class for Storing Microarray Experiment Information
notes<-,eSet,list-method | Class to Contain High-Throughput Assays and Experimental Metadata
notes<-,exprSet-method | Class for Microarray Data and Methods for Processing Them
notes<-,MIAME,list-method | Class for Storing Microarray Experiment Information

## -- O --

openPDF | Open PDF Files in a Standard Viewer
openVignette | Open a Vignette or Show Vignette Selection Menu
otherInfo,MIAME-method | Class for Storing Microarray Experiment Information

## -- P --

package.version | Report Version of a Package
pData | Retrieve information on experimental phenotypes recorded in eSet and exprSet-derived classes.
pData,AnnotatedDataFrame-method | Class to Contain Measured Variables and Their Meta-Data Description.
pData,annotatedDataset-method | Virtual Superset for 'exprSet', 'eSet' etc.
pData,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
pData,phenoData-method | Class For Patient or Experiment Level Data
pData<-,AnnotatedDataFrame,data.frame-method | Class to Contain Measured Variables and Their Meta-Data Description.
pData<-,annotatedDataset,ANY-method | Virtual Superset for 'exprSet', 'eSet' etc.
pData<-,eSet,data.frame-method | Class to Contain High-Throughput Assays and Experimental Metadata
pData<-,phenoData,ANY-method | Class For Patient or Experiment Level Data
phenoData | Retrieve information on experimental phenotypes recorded in eSet and exprSet-derived classes.
phenoData,annotatedDataset-method | Virtual Superset for 'exprSet', 'eSet' etc.
phenoData,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
phenoData-class | Class For Patient or Experiment Level Data
phenoData<-,annotatedDataset,phenoData-method | Class For Patient or Experiment Level Data
phenoData<-,eSet,AnnotatedDataFrame-method | Class to Contain High-Throughput Assays and Experimental Metadata
preproc,MIAME-method | Class for Storing Microarray Experiment Information
pubMedIds | Retrieve feature and sample names from eSets and exprSets.
pubMedIds,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
pubMedIds,MIAME-method | Class for Storing Microarray Experiment Information
pubMedIds<-,eSet,character-method | Class to Contain High-Throughput Assays and Experimental Metadata
pubMedIds<-,MIAME,ANY-method | Class for Storing Microarray Experiment Information

## -- R --

read.exprSet | Read Experimental Data and into an 'exprSet' Object
read.MIAME | Read MIAME Information into an Instance of Class 'MIAME'
read.phenoData | Read 'phenoData'
reporter | Example Data Frame Object for the ReporterInfo Slot
reporterInfo | Retrieve and set information about reporters.
reporterInfo,annotatedDataset-method | Virtual Superset for 'exprSet', 'eSet' etc.
reporterInfo<-,annotatedDataset,data.frame-method | Virtual Superset for 'exprSet', 'eSet' etc.
reporterNames,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
reverseSplit | A function to reverse the role of names and values in a list.
rowMax | A function to compute empirical row quantiles.
rowMedians | A function to compute empirical row quantiles.
rowMin | A function to compute empirical row quantiles.
rowQ | A function to compute empirical row quantiles.

## -- S --

sample.eSet | Dataset of class 'eSet'
sample.ExpressionSet | Dataset of class 'ExpressionSet'
sample.exprSet | Dataset of class 'exprSet'
sample.exprSet.1 | Dataset of class 'exprSet'
sampleNames | Retrieve feature and sample names from eSets and exprSets.
sampleNames,AnnotatedDataFrame-method | Class to Contain Measured Variables and Their Meta-Data Description.
sampleNames,AssayData-method | Class "AssayData"
sampleNames,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
sampleNames,exprSet-method | Class for Microarray Data and Methods for Processing Them
sampleNames<-,AnnotatedDataFrame-method | Class to Contain Measured Variables and Their Meta-Data Description.
sampleNames<-,AssayData-method | Class "AssayData"
sampleNames<-,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
sampleNames<-,exprSet-method | Class for Microarray Data and Methods for Processing Them
samples | Class for Storing Microarray Experiment Information
samples,MIAME-method | Class for Storing Microarray Experiment Information
se.exprs | Retrieve expression data from eSets.
se.exprs,exprSet-method | Class for Microarray Data and Methods for Processing Them
se.exprs<-,exprSet-method | Class for Microarray Data and Methods for Processing Them
seD | A subset of some expression data.
show,AnnotatedDataFrame-method | Class to Contain Measured Variables and Their Meta-Data Description.
show,container-method | A Lockable List Structure with Constraints on Content
show,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
show,exprSet-method | Class for Microarray Data and Methods for Processing Them
show,MIAME-method | Class for Storing Microarray Experiment Information
show,phenoData-method | Class For Patient or Experiment Level Data
SnpSet | Class to Contain Objects Describing High-Throughput SNP Assays.
SnpSet-class | Class to Contain Objects Describing High-Throughput SNP Assays.
split | Class for Microarray Data and Methods for Processing Them
split,exprSet,factor,missing-method | Class for Microarray Data and Methods for Processing Them
split,exprSet,vector,missing-method | Class for Microarray Data and Methods for Processing Them
split,phenoData,vector,missing-method | Class For Patient or Experiment Level Data
storageMode | Retrieve or set storage mode for eSets.
storageMode,AssayData-method | Class "AssayData"
storageMode,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
storageMode<-,AssayData,character-method | Class "AssayData"
storageMode<-,eSet,character-method | Class to Contain High-Throughput Assays and Experimental Metadata
strbreak | Break Character Strings to Fit Width
SW | Class to Contain High-Throughput Assays and Experimental Metadata
SWPD | Class to Contain High-Throughput Assays and Experimental Metadata
swrep | Class to Contain High-Throughput Assays and Experimental Metadata

## -- T --

testBioCConnection | A function to check internet connectivity to Bioconductor

## -- U --

update2MIAME | Class for Microarray Data and Methods for Processing Them
update2MIAME,exprSet-method | Class for Microarray Data and Methods for Processing Them
updateOldESet | Update previously created eSet object to current eSet structure

## -- V --

varLabels | Retrieve information on experimental phenotypes recorded in eSet and exprSet-derived classes.
varLabels,AnnotatedDataFrame-method | Class to Contain Measured Variables and Their Meta-Data Description.
varLabels,annotatedDataset-method | Virtual Superset for 'exprSet', 'eSet' etc.
varLabels,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
varLabels,phenoData-method | Class For Patient or Experiment Level Data
varLabels<-,AnnotatedDataFrame-method | Class to Contain Measured Variables and Their Meta-Data Description.
varLabels<-,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
varMetadata | Retrieve information on experimental phenotypes recorded in eSet and exprSet-derived classes.
varMetadata,AnnotatedDataFrame-method | Class to Contain Measured Variables and Their Meta-Data Description.
varMetadata,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
varMetadata,phenoData-method | Class For Patient or Experiment Level Data
varMetadata<-,AnnotatedDataFrame,data.frame-method | Class to Contain Measured Variables and Their Meta-Data Description.
varMetadata<-,eSet,data.frame-method | Class to Contain High-Throughput Assays and Experimental Metadata

## -- W --

write.exprs | Class for Microarray Data and Methods for Processing Them
write.exprs,exprSet-method | Class for Microarray Data and Methods for Processing Them

## -- misc --

[,AnnotatedDataFrame-method | Class to Contain Measured Variables and Their Meta-Data Description.
[,container-method | A Lockable List Structure with Constraints on Content
[,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
[,exprSet-method | Class for Microarray Data and Methods for Processing Them
[,phenoData-method | Class For Patient or Experiment Level Data
[[,AnnotatedDataFrame-method | Class to Contain Measured Variables and Their Meta-Data Description.
[[,annotatedDataset-method | Virtual Superset for 'exprSet', 'eSet' etc.
[[,container-method | A Lockable List Structure with Constraints on Content
[[,phenoData-method | Class For Patient or Experiment Level Data
[[<-,AnnotatedDataFrame-method | Class to Contain Measured Variables and Their Meta-Data Description.
[[<-,annotatedDataset-method | Virtual Superset for 'exprSet', 'eSet' etc.
[[<-,container-method | A Lockable List Structure with Constraints on Content
[[<-,phenoData-method | Class For Patient or Experiment Level Data