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

new('ExpressionSet', phenoData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], exprs = [matrix], ...)

as([exprSet],"ExpressionSet")

ExpressionSet instances are usually created through new("ExpressionSet", ...). Usually the arguments to new include exprs (a matrix of expression data, with features corresponding to rows and samples to columns), phenoData, experimentData, and annotation. phenoData, experimentData, and annotation 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

experimentData:

See eSet

annotation:

See eSet

Methods

Class-specific methods.

as(exprSet,"ExpressionSet")

Coerce objects of exprSet-class to ExpressionSet

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

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

Derived from 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

combine(ExpressionSet,ExpressionSet):

See eSet

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

See eSet

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

DEPRECATED

Standard generic methods:

initialize(ExpressionSet):

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

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.

show(ExpressionSet)

See eSet

dim(ExpressionSet), ncol

See eSet

ExpressionSet[(index):

See eSet

ExpressionSet$, ExpressionSet$<-

See eSet

Author(s)

Biocore team

See Also

eSet-class, ExpressionSet-class

Examples

# create an instance of ExpressionSet
new("ExpressionSet")

# update existing exprSet-like class to ExpressionSet
data(sample.exprSet)
expressionSet <- as(sample.exprSet,"ExpressionSet")
expressionSet

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

# subset: first 10 genes, samples 2, 4, and 10
expressionSet <- as(sample.exprSet,"ExpressionSet")
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]