Biobase: Biobase: Base functions for Bioconductor

Functions that are needed by many other packages or which replace R functions.

AuthorR. Gentleman, V. Carey, M. Morgan, S. Falcon
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version2.34.0

View on Bioconductor

Man pages

abstract: Retrieve Meta-data from eSets and ExpressionSets.

addVig2Menu: Add Menu Items to an Existing/New Menu of Window

Aggregate: A Simple Aggregation Mechanism.

annotatedDataFrameFrom-methods: Methods for Function annotatedDataFrameFrom in Package...

anyMissing: Checks if there are any missing values in an object or not

assayData: Retrieve assay data from eSets and ExpressionSets.

Biobase-package: Biobase Package Overview

cache: Evaluate an expression if its value is not already cached.

channel: Create a new ExpressionSet instance by selecting a specific...

channelNames: Retrieve and set channel names from object

class.aggregator: A Simple Class for Aggregators

class.AnnotatedDataFrame: Class Containing Measured Variables and Their Meta-Data...

class.AssayData: Class "AssayData"

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...

class.ExpressionSet: Class to Contain and Describe High-Throughput Expression...

class.MIAME: Class for Storing Microarray Experiment Information

class.MIAxE: MIAxE objects

class.MultiSet: Class to Contain and Describe High-Throughput Expression...

class.NChannelSet: Class to contain data from multiple channel array...

class.SnpSet: Class to Contain Objects Describing High-Throughput SNP...

classVersion: Retrieve information about versioned classes

class.Versioned: Class "Versioned"

class.VersionedBiobase: Class "VersionedBiobase"

class.Versions: Class "Versions"

class.VersionsNull: Class "VersionsNull"

contents: Function to retrieve contents of environments

copyEnv: List-Environment interactions

copySubstitute: Copy Between Connections or Files with Configure-Like...

createPackage: Create a Package Directory from a Template

data.aaMap: Dataset: Names and Characteristics of Amino Acids

data.geneData: Sample expression matrix and phenotype data.frames.

data.reporter: Example data.frame representing reporter information

data.sample.ExpressionSet: Dataset of class 'ExpressionSet'

data.sample.MultiSet: Data set of class 'MultiSet'

defunct: Biobase Deprecated and Defunct

description: Retrieve and set overall experimental information eSet-like...

dims: Retrieve dimensions of all elements in a list or environment

dumpPackTxt: Dump Textual Description of a Package

esApply: An apply-like function for ExpressionSet and related...

exprs: Retrieve expression data from eSets.

featureData: Retrieve information on features recorded in eSet-derived...

featureNames: Retrieve feature and sample names from eSets.

getPkgVigs: List Vignette Files for a Package

internals: Internals

isCurrent: Use version information to test whether class is current

isUnique: Determine Unique Elements

isVersioned: Determine whether object or class contains versioning...

lcSuffix: Compute the longest common prefix or suffix of a string

listLen: Lengths of list elements

makeDataPackage: Make an R package from a data object

matchpt: Nearest neighbor search.

multiassign: Assign Values to a Names

note: Informational Messages

notes: Retrieve and set eSet notes.

openPDF: Open PDF Files in a Standard Viewer

openVignette: Open a Vignette or Show Vignette Selection Menu

package.version: Report Version of a Package

phenoData: Retrieve information on experimental phenotypes recorded in...

protocolData: Protocol Metadata

read.AnnotatedDataFrame: Read and write 'AnnotatedDataFrame'

readExpressionSet: Read 'ExpressionSet'

read.MIAME: Read MIAME Information into an Instance of Class 'MIAME'

reverseSplit: A function to reverse the role of names and values in a list.

rowMedians: Calculates the median for each row in a matrix

rowQ: A function to compute empirical row quantiles.

ScalarObject-class: Utility classes for length one (scalar) objects

selectChannels: Create a new NChannelSet instance by selecting specific...

selectSome: Extract elements of a vector for concise rendering

snpCall: Get and retrieve SNP call and call probability data.

storageMode: Retrieve or set storage mode for eSets.

strbreak: Break Character Strings to Fit Width

subListExtract: Extract the same element from the sublists of a list

testBioCConnection: A function to check internet connectivity to Bioconductor

updateObjectTo: Update an object to the class definition of a template

updateOldESet: Update previously created eSet object to current eSet...

userQuery: A function to query the user for input

validMsg: Conditionally append result to validity message

Functions

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

Files

Biobase/DESCRIPTION
Biobase/NAMESPACE
Biobase/NEWS
Biobase/R
Biobase/R/AllGenerics.R Biobase/R/DataClasses.R Biobase/R/VersionedClasses.R Biobase/R/VersionsClass.R Biobase/R/anyMissing.R Biobase/R/environment.R Biobase/R/methods-AnnotatedDataFrame.R Biobase/R/methods-AssayData.R Biobase/R/methods-ExpressionSet.R Biobase/R/methods-MIAME.R Biobase/R/methods-MIAxE.R Biobase/R/methods-MultiSet.R Biobase/R/methods-NChannelSet.R Biobase/R/methods-ScalarObject.R Biobase/R/methods-SnpSet.R Biobase/R/methods-VersionedClass.R Biobase/R/methods-VersionsNull.R Biobase/R/methods-aggregator.R Biobase/R/methods-container.R Biobase/R/methods-eSet.R Biobase/R/packages.R Biobase/R/rowOp-methods.R Biobase/R/strings.R Biobase/R/tools.R Biobase/R/updateObjectTo.R Biobase/R/vignettes.R Biobase/R/zzz.R
Biobase/build
Biobase/build/vignette.rds
Biobase/data
Biobase/data/SW.rda
Biobase/data/aaMap.R
Biobase/data/geneCov.R
Biobase/data/geneCovariate.rda
Biobase/data/geneData.R
Biobase/data/reporter.rda
Biobase/data/sample.ExpressionSet.rda
Biobase/data/sample.MultiSet.rda
Biobase/data/sample.eSet.R
Biobase/data/sample.exprSet.1.R
Biobase/data/sample.exprSet.R
Biobase/data/seD.rda
Biobase/inst
Biobase/inst/CITATION
Biobase/inst/Code
Biobase/inst/Code/DESCRIPTION
Biobase/inst/Code/R
Biobase/inst/Code/R/get@PKGNAME@.R
Biobase/inst/Code/man
Biobase/inst/Code/man/@PKGNAME@.Rd
Biobase/inst/Code/man/get@PKGNAME@.Rd
Biobase/inst/ExpressionSet
Biobase/inst/ExpressionSet/DESCRIPTION
Biobase/inst/ExpressionSet/man
Biobase/inst/ExpressionSet/man/@PKGNAME@.Rd
Biobase/inst/doc
Biobase/inst/doc/BiobaseDevelopment.R
Biobase/inst/doc/BiobaseDevelopment.Rnw
Biobase/inst/doc/BiobaseDevelopment.pdf
Biobase/inst/doc/ExpressionSetIntroduction.R
Biobase/inst/doc/ExpressionSetIntroduction.Rnw
Biobase/inst/doc/ExpressionSetIntroduction.pdf
Biobase/inst/doc/esApply.R
Biobase/inst/doc/esApply.Rnw
Biobase/inst/doc/esApply.pdf
Biobase/inst/extdata
Biobase/inst/extdata/exprsData.txt
Biobase/inst/extdata/pData.txt
Biobase/inst/scripts
Biobase/inst/scripts/esetTesting.R
Biobase/inst/scripts/getBioC.R
Biobase/inst/scripts/getBioCHelp
Biobase/inst/scripts/getBioCPkgNames.R
Biobase/inst/scripts/makeExpressionSetPackage.R
Biobase/inst/scripts/query.packages.R
Biobase/inst/testClass.R
Biobase/inst/unitTests
Biobase/inst/unitTests/VersionedClass_data
Biobase/inst/unitTests/VersionedClass_data/1.8
Biobase/inst/unitTests/VersionedClass_data/1.8/AnnotatedDataFrame.Rda
Biobase/inst/unitTests/VersionedClass_data/1.8/ExpressionSet.Rda
Biobase/inst/unitTests/VersionedClass_data/1.8/MIAME.Rda
Biobase/inst/unitTests/VersionedClass_data/1.8/exprSet.Rda
Biobase/inst/unitTests/VersionedClass_data/1.8/phenoData.Rda
Biobase/inst/unitTests/VersionedClass_data/2.0
Biobase/inst/unitTests/VersionedClass_data/2.0/AnnotatedDataFrame.Rda
Biobase/inst/unitTests/VersionedClass_data/2.0/ExpressionSet.Rda
Biobase/inst/unitTests/VersionedClass_data/2.0/MIAME.Rda
Biobase/inst/unitTests/VersionedClass_data/2.0/MultiSet.Rda
Biobase/inst/unitTests/VersionedClass_data/2.0/ScalarCharacter.Rda
Biobase/inst/unitTests/VersionedClass_data/2.0/SnpSet.Rda
Biobase/inst/unitTests/VersionedClass_data/2.0/Versioned.Rda
Biobase/inst/unitTests/VersionedClass_data/2.0/VersionedBiobase.Rda
Biobase/inst/unitTests/VersionedClass_data/2.0/Versions.Rda
Biobase/inst/unitTests/VersionedClass_data/2.0/VersionsNull.Rda
Biobase/inst/unitTests/VersionedClass_data/2.0/aggregator.Rda
Biobase/inst/unitTests/VersionedClass_data/2.0/container.Rda
Biobase/inst/unitTests/VersionedClass_data/2.0/exprSet.Rda
Biobase/inst/unitTests/VersionedClass_data/2.0/phenoData.Rda
Biobase/inst/unitTests/VersionedClass_data/devel
Biobase/inst/unitTests/VersionedClass_data/devel/AnnotatedDataFrame.Rda
Biobase/inst/unitTests/VersionedClass_data/devel/ExpressionSet.Rda
Biobase/inst/unitTests/VersionedClass_data/devel/MIAME.Rda
Biobase/inst/unitTests/VersionedClass_data/devel/MultiSet.Rda
Biobase/inst/unitTests/VersionedClass_data/devel/NChannelSet.Rda
Biobase/inst/unitTests/VersionedClass_data/devel/SWPD.rda
Biobase/inst/unitTests/VersionedClass_data/devel/ScalarCharacter.Rda
Biobase/inst/unitTests/VersionedClass_data/devel/ScalarInteger.Rda
Biobase/inst/unitTests/VersionedClass_data/devel/ScalarLogical.Rda
Biobase/inst/unitTests/VersionedClass_data/devel/ScalarNumeric.Rda
Biobase/inst/unitTests/VersionedClass_data/devel/SnpSet.Rda
Biobase/inst/unitTests/VersionedClass_data/devel/Versioned.Rda
Biobase/inst/unitTests/VersionedClass_data/devel/VersionedBiobase.Rda
Biobase/inst/unitTests/VersionedClass_data/devel/Versions.Rda
Biobase/inst/unitTests/VersionedClass_data/devel/VersionsNull.Rda
Biobase/inst/unitTests/VersionedClass_data/devel/aggregator.Rda
Biobase/inst/unitTests/VersionedClass_data/devel/bbsym.rda
Biobase/inst/unitTests/VersionedClass_data/devel/container.Rda
Biobase/inst/unitTests/VersionedClass_data/devel/eset.rda
Biobase/inst/unitTests/VersionedClass_data/devel/exprSet.Rda
Biobase/inst/unitTests/VersionedClass_data/devel/golubMergeSub.rda
Biobase/inst/unitTests/VersionedClass_data/devel/sample.eSet.rda
Biobase/inst/unitTests/VersionedClass_data/devel/sample.exprSet.1.rda
Biobase/inst/unitTests/VersionedClass_data/devel/sample.exprSet.rda
Biobase/inst/unitTests/VersionedClass_data/devel/swrep.rda
Biobase/inst/unitTests/VersionedClass_data/raw
Biobase/inst/unitTests/VersionedClass_data/raw/exprs.tab
Biobase/inst/unitTests/VersionedClass_data/raw/pData.tab
Biobase/inst/unitTests/VersionedClass_data/raw/varMetadata.tab
Biobase/inst/unitTests/test_AnnotatedDataFrame.R
Biobase/inst/unitTests/test_AssayData.R
Biobase/inst/unitTests/test_DataClasses.R
Biobase/inst/unitTests/test_EsetSubclasses.R
Biobase/inst/unitTests/test_ExpressionSet.R
Biobase/inst/unitTests/test_NChannelSet.R
Biobase/inst/unitTests/test_SnpSet.R
Biobase/inst/unitTests/test_UpdateObject.R
Biobase/inst/unitTests/test_VersionedClass.R
Biobase/inst/unitTests/test_cache.R
Biobase/inst/unitTests/test_checkClass.R
Biobase/inst/unitTests/test_combine.R
Biobase/inst/unitTests/test_copyEnv.R
Biobase/inst/unitTests/test_esApply.R
Biobase/inst/unitTests/test_subListExtract.R
Biobase/inst/unitTests/test_unsaveSetSlot.R
Biobase/inst/unitTests/utilities.R
Biobase/man
Biobase/man/Aggregate.Rd Biobase/man/Biobase-package.Rd Biobase/man/ScalarObject-class.Rd Biobase/man/abstract.Rd Biobase/man/addVig2Menu.Rd Biobase/man/annotatedDataFrameFrom-methods.Rd Biobase/man/anyMissing.Rd Biobase/man/assayData.Rd Biobase/man/cache.Rd Biobase/man/channel.Rd Biobase/man/channelNames.Rd Biobase/man/class.AnnotatedDataFrame.Rd Biobase/man/class.AssayData.Rd Biobase/man/class.ExpressionSet.Rd Biobase/man/class.MIAME.Rd Biobase/man/class.MIAxE.Rd Biobase/man/class.MultiSet.Rd Biobase/man/class.NChannelSet.Rd Biobase/man/class.SnpSet.Rd Biobase/man/class.Versioned.Rd Biobase/man/class.VersionedBiobase.Rd Biobase/man/class.Versions.Rd Biobase/man/class.VersionsNull.Rd Biobase/man/class.aggregator.Rd Biobase/man/class.characterORmiame.Rd Biobase/man/class.container.Rd Biobase/man/class.eSet.Rd Biobase/man/classVersion.Rd Biobase/man/contents.Rd Biobase/man/copyEnv.Rd Biobase/man/copySubstitute.Rd Biobase/man/createPackage.Rd Biobase/man/data.aaMap.Rd Biobase/man/data.geneData.Rd Biobase/man/data.reporter.Rd Biobase/man/data.sample.ExpressionSet.Rd Biobase/man/data.sample.MultiSet.Rd Biobase/man/defunct.Rd Biobase/man/description.Rd Biobase/man/dims.Rd Biobase/man/dumpPackTxt.Rd Biobase/man/esApply.Rd Biobase/man/exprs.Rd Biobase/man/featureData.Rd Biobase/man/featureNames.Rd Biobase/man/getPkgVigs.Rd Biobase/man/internals.Rd Biobase/man/isCurrent.Rd Biobase/man/isUnique.Rd Biobase/man/isVersioned.Rd Biobase/man/lcSuffix.Rd Biobase/man/listLen.Rd Biobase/man/makeDataPackage.Rd Biobase/man/matchpt.Rd Biobase/man/multiassign.Rd Biobase/man/note.Rd Biobase/man/notes.Rd Biobase/man/openPDF.Rd Biobase/man/openVignette.Rd Biobase/man/package.version.Rd Biobase/man/phenoData.Rd Biobase/man/protocolData.Rd Biobase/man/read.AnnotatedDataFrame.Rd Biobase/man/read.MIAME.Rd Biobase/man/readExpressionSet.Rd Biobase/man/reverseSplit.Rd Biobase/man/rowMedians.Rd Biobase/man/rowQ.Rd Biobase/man/selectChannels.Rd Biobase/man/selectSome.Rd Biobase/man/snpCall.Rd Biobase/man/storageMode.Rd Biobase/man/strbreak.Rd Biobase/man/subListExtract.Rd Biobase/man/testBioCConnection.Rd Biobase/man/updateObjectTo.Rd Biobase/man/updateOldESet.Rd Biobase/man/userQuery.Rd Biobase/man/validMsg.Rd
Biobase/src
Biobase/src/Rinit.c
Biobase/src/anyMissing.c
Biobase/src/envir.c
Biobase/src/matchpt.c
Biobase/src/rowMedians.c
Biobase/src/rowMedians_TYPE-template.h
Biobase/src/sublist_extract.c
Biobase/src/templates-types.h
Biobase/src/templates-types_undef.h
Biobase/tests
Biobase/tests/test-all.R
Biobase/tests/test-rowMedians.R
Biobase/vignettes
Biobase/vignettes/BiobaseDevelopment.Rnw
Biobase/vignettes/ExpressionSetIntroduction.Rnw
Biobase/vignettes/esApply.Rnw
Biobase/vignettes/legacy
Biobase/vignettes/legacy/Biobase.Rnw
Biobase/vignettes/legacy/Bioconductor.Rnw
Biobase/vignettes/legacy/HowTo.Rnw
Biobase/vignettes/legacy/Qviews.Rnw

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