MultiSet {Biobase}R Documentation

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

Description

Container for high-throughput assays and experimental metadata. MutliSet is derived from eSet-class. MultiSet differs from ExpressionSet-class because MultiSet can contain any element(s) in assayData (ExpressionSet must have an element named exprs).

Extends

Directly extends class eSet.

Creating Objects

new('MultiSet', phenoData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], ...)

updateOldESet(oldESet,"MultiSet")

MultiSet instances are usually created through new("MultiSet", ...). The ... arguments to new are matrices 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.

updateOldESet will take a serialized instance (e.g., saved to a disk file with save object created with earlier definitions of the eSet-class, and update the object to MultiSet. Warnings are issued when direct translation is not possible; incorrectly created oldESet instances may not be updated.

Slots

Inherited from eSet:

assayData:
Contains zero or more matrices with equal dimensions, and with column number equal to nrow(phenoData). Each matrix in assayData has rows represening features (e.g., reporters) and columns representing samples. Class:AssayData-class
phenoData:
See eSet-class
experimentData:
See eSet-class
annotation:
See eSet-class

Methods

Class-specific methods: none

Derived from eSet-class:

sampleNames(MultiSet) and sampleNames(MultiSet)<-:
See eSet-class
featureNames(MultiSet), featureNames(MultiSet, value)<-:
See eSet-class
dims(MultiSet):
See eSet-class
phenoData(MultiSet), phenoData(MultiSet,value)<-:
See eSet-class
varLabels(MultiSet), varLabels(MultiSet, value)<-:
See eSet-class
varMetadata(MultiSet), varMetadata(MultiSet,value)<-:
See eSet-class
pData(MultiSet), pData(MultiSet,value)<-:
See eSet-class
varMetadata(MultiSet), varMetadata(MultiSet,value)
See eSet-class
experimentData(MultiSet),experimentData(MultiSet,value)<-:
See eSet-class
pubMedIds(MultiSet), pubMedIds(MultiSet,value)
See eSet-class
abstract(MultiSet):
See eSet-class
annotation(MultiSet), annotation(MultiSet,value)<-
See eSet-class
combine(MultiSet,MultiSet):
See eSet-class
storageMode(eSet), storageMode(eSet,character)<-:
See eSet-class
reporterNames(MultiSet), reporterNames(MultiSet,value)<-:
DEPRECATED

Standard generic methods:

initialize(MultiSet):
Object instantiation, used by new; not to be called directly by the user.
validObject(MultiSet):
Validity-checking method, ensuring that all elements of assayData are matricies with equal dimensions.
show(MultiSet)
See eSet-class
dim(MultiSet), ncol
See eSet-class
MultiSet[(index):
See eSet-class
MultiSet$, MultiSet$<-
See eSet-class

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]

[Package Biobase version 1.10.1 Index]