ExpressionSet {Biobase}R Documentation

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")

new("ExpressionSet", phenoData = new("AnnotatedDataFrame"), featureData = new("AnnotatedDataFrame"), experimentData = new("MIAME"), annotation = character(0), protocolData = phenoData[,integer(0)], exprs = new("matrix"))

This creates an ExpressionSet with assayData implicitly created to contain exprs. Additional named matrix arguments with the same dimensions as exprs are added to assayData; the row and column names of these additional matricies should match those of exprs.

new("ExpressionSet", assayData = assayDataNew(exprs=new("matrix")), phenoData = new("AnnotatedDataFrame"), featureData = new("AnnotatedDataFrame"), experimentData = new("MIAME"), annotation = character(0), protocolData = phenoData[,integer(0)])

This creates an ExpressionSet with assayData provided explicitly. In this form, the only required named argument is assayData.

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, featureData, experimentData, annotation, and protocolData. 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
new("ExpressionSet")

new("ExpressionSet",
    exprs=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)

[Package Biobase version 2.10.0 Index]