Class to Contain and Describe High-Throughput Expression Level Assays.

Description

Container for high-throughput assays and experimental metadata. ExpressionSet class is derived from eSet, and requires a matrix named exprs as assayData member.

Usage

## Instance creation
ExpressionSet(assayData,
    phenoData=annotatedDataFrameFrom(assayData, byrow=FALSE),
    featureData=annotatedDataFrameFrom(assayData, byrow=TRUE),
    experimentData=MIAME(), annotation=character(),
    protocolData=annotatedDataFrameFrom(assayData, byrow=FALSE),
    ...)

## Additional methods documented below

Arguments

Extends

Directly extends class eSet.

Creating Objects

ExpressionSet instances are usually created through ExpressionSet().

Slots

Inherited from eSet:

assayData:

Contains matrices with equal dimensions, and with column number equal to nrow(phenoData). assayData must contain a matrix exprs with rows representing features (e.g., probe sets) and columns representing samples. Additional matrices of identical size (e.g., representing measurement errors) may also be included in assayData. Class:AssayData-class

phenoData:

See eSet

featureData:

See eSet

experimentData:

See eSet

annotation:

See eSet

protocolData:

See eSet

Methods

Class-specific methods.

as(exprSet,"ExpressionSet")

Coerce objects of exprSet-class to ExpressionSet

as(object,"data.frame")

Coerce objects of ExpressionSet-class to data.frame by transposing the expression matrix and concatenating phenoData

exprs(ExpressionSet), exprs(ExpressionSet,matrix)<-

Access and set elements named exprs in the AssayData-class slot.

esApply(ExpressionSet, MARGIN, FUN, ...)

'apply'-like function to conveniently operate on ExpressionSet objects. See esApply.

write.exprs(ExpressionSet)

Write expression values to a text file. It takes the same arguments as write.table

Derived from eSet:

updateObject(object, ..., verbose=FALSE)

Update instance to current version, if necessary. See updateObject and eSet

isCurrent(object)

Determine whether version of object is current. See isCurrent

isVersioned(object)

Determine whether object contains a 'version' string describing its structure . See isVersioned

assayData(ExpressionSet):

See eSet

sampleNames(ExpressionSet) and sampleNames(ExpressionSet)<-:

See eSet

featureNames(ExpressionSet), featureNames(ExpressionSet, value)<-:

See eSet

dims(ExpressionSet):

See eSet

phenoData(ExpressionSet), phenoData(ExpressionSet,value)<-:

See eSet

varLabels(ExpressionSet), varLabels(ExpressionSet, value)<-:

See eSet

varMetadata(ExpressionSet), varMetadata(ExpressionSet,value)<-:

See eSet

pData(ExpressionSet), pData(ExpressionSet,value)<-:

See eSet

varMetadata(ExpressionSet), varMetadata(ExpressionSet,value)

See eSet

experimentData(ExpressionSet),experimentData(ExpressionSet,value)<-:

See eSet

pubMedIds(ExpressionSet), pubMedIds(ExpressionSet,value)

See eSet

abstract(ExpressionSet):

See eSet

annotation(ExpressionSet), annotation(ExpressionSet,value)<-

See eSet

protocolData(ExpressionSet), protocolData(ExpressionSet,value)<-

See eSet

combine(ExpressionSet,ExpressionSet):

See eSet

storageMode(ExpressionSet), storageMode(ExpressionSet,character)<-:

See eSet

Standard generic methods:

initialize(ExpressionSet):

Object instantiation, used by new; not to be called directly by the user.

updateObject(ExpressionSet):

Update outdated versions of ExpressionSet to their current definition. See updateObject, Versions-class.

validObject(ExpressionSet):

Validity-checking method, ensuring that exprs is a member of assayData. checkValidity(ExpressionSet) imposes this validity check, and the validity checks of eSet.

makeDataPackage(object, author, email, packageName, packageVersion, license, biocViews, filePath, description=paste(abstract(object), collapse="\n\n"), ...)

Create a data package based on an ExpressionSet object. See makeDataPackage.

as(exprSet,ExpressionSet):

Coerce exprSet to ExpressionSet.

as(eSet,ExpressionSet):

Coerce the eSet portion of an object to ExpressionSet.

show(ExpressionSet)

See eSet

dim(ExpressionSet), ncol

See eSet

ExpressionSet[(index):

See eSet

ExpressionSet$, ExpressionSet$<-

See eSet

ExpressionSet[[i]], ExpressionSet[[i]]<-

See eSet

Author(s)

Biocore team

See Also

eSet-class, ExpressionSet-class.

Examples

# create an instance of ExpressionSet
ExpressionSet()

ExpressionSet(assayData=matrix(runif(1000), nrow=100, ncol=10))

# update an existing ExpressionSet
data(sample.ExpressionSet)
updateObject(sample.ExpressionSet)

# information about assay and sample data
featureNames(sample.ExpressionSet)[1:10]
sampleNames(sample.ExpressionSet)[1:5]
experimentData(sample.ExpressionSet)

# subset: first 10 genes, samples 2, 4, and 10
expressionSet <- sample.ExpressionSet[1:10,c(2,4,10)]

# named features and their expression levels
subset <- expressionSet[c("AFFX-BioC-3_at","AFFX-BioDn-5_at"),]
exprs(subset)

# samples with above-average 'score' in phenoData
highScores <- expressionSet$score > mean(expressionSet$score)
expressionSet[,highScores]

# (automatically) coerce to data.frame
lm(score~AFFX.BioDn.5_at + AFFX.BioC.3_at, data=subset)