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.

Extends

Directly extends class eSet.

Creating Objects

ExpressionSet instances are usually created through

ExpressionSet()

ExpressionSet(assayData, phenoData=annotatedDataFrameFrom(assayData, byrow=FALSE), featureData=annotatedDataFrameFrom(assayData, byrow=TRUE), experimentData=new("MIAME"), annotation=character(), protocolData=annotatedDataFrameFrom(assayData, byrow=FALSE), ...) This creates an ExpressionSet with assayData provided explicitly. In this form, the only required named argument is assayData. assayData can be matrix (a matrix of expression data, with features corresponding to rows and samples to columns) or an environment that contains exprs.

phenoData, featureData, experimentData, annotation, and protocolData can be missing, in which case they are assigned default values.

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 represening features (e.g., reporters) 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]
phenoData(sample.ExpressionSet)
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)