ExpressionSetIllumina {beadarray}R Documentation

Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.

Description

Container for high-throughput assays and experimental metadata. ExpressionSetIllumina class is derived from eSet, and requires matrices exprs, se.exprs, NoBeads, Detection as assay data members.

Extends

Directly extends class eSet.

Creating Objects

new('ExpressionSetIllumina', phenoData = [AnnotatedDataFrame], exprs = [matrix], se.exprs = [matrix], NoBeads = [matrix], Detection = [matrix], annotation = [character], featureData = [AnnotatedDataFrame], experimentData = [MIAME], ...) ExpressionSetIllumina instances are usually created through new("ExpressionSetIllumina", ...). Arguments to new include exprs, se.exprs, NoBeads, Detection, 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 representing features (e.g., genes) and columns representing samples, a matrix se.exprs describing the standard error of each gene, and matrices NoBeads and Detection to describe the number of beads used to produce the summary and a probability of a gene being expressed above background. The contents of these matrices are not enforced by the class. Additional matrices of identical size may also be included in assayData. Class:AssayData
phenoData:
See eSet
experimentData:
See eSet
annotation:
See eSet
featureData:
annotation for SNPs, usually will contain a CHR and a MapInfo column for genomic localization

Methods

Class-specific methods:

exprs(ExpressionSetIllumina), exprs(ExpressionSetIllumina,matrix)<-
Access and set elements named exprs in the AssayData slot.
se.exprs(ExpressionSetIllumina), se.exprs(ExpressionSetIllumina,matrix)<-
Access and set elements named se.exprs in the AssayData slot.
NoBeads(ExpressionSetIllumina)
Access elements named NoBeads in the AssayData slot.
Detection(ExpressionSetIllumina)
Access elements named Detection in the AssayData slot.
getVariance(ExpressionSetIllumina)
Calculate bead-type specific variance using se.exprs and NoBeads from the AssayData slot.
QCInfo(ExpressionSetIllumina),QCInfo(ExpressionSetIllumina,list)<-
Access elements named QC in the AssayData slot.
object[(index):
Conducts subsetting of matrices and phenoData and reporterInfo components
combine(ExpressionSetIllumina,ExpressionSetIllumina):
performs union-like combination in both dimensions of ExpressionSetIllumina objects
show(ExpressionSetSetIllumina)
See eSet

Derived from eSet:

sampleNames(ExpressionSetSetIllumina) and sampleNames(ExpressionSetSetIllumina)<-:
See eSet
featureNames(ExpressionSetSetIllumina), featureNames(ExpressionSetSetIllumina, value)<-:
See eSet
dims(ExpressionSetSetIllumina):
See eSet
phenoData(ExpressionSetSetIllumina), phenoData(ExpressionSetSetIllumina,value)<-:
See eSet
varLabels(ExpressionSetSetIllumina), varLabels(ExpressionSetSetIllumina, value)<-:
See eSet
varMetadata(ExpressionSetSetIllumina), varMetadata(ExpressionSetSetIllumina,value)<-:
See eSet
pData(ExpressionSetSetIllumina), pData(ExpressionSetSetIllumina,value)<-:
See eSet
varMetadata(ExpressionSetSetIllumina), varMetadata(ExpressionSetSetIllumina,value)
See eSet
experimentData(ExpressionSetSetIllumina),experimentData(ExpressionSetSetIllumina,value)<-:
See eSet
annotation(ExpressionSetSetIllumina), annotation(ExpressionSetSetIllumina,value)<-
See eSet
storageMode(eSet), storageMode(eSet,character)<-:
See eSet

Standard generic methods:

initialize(ExpressionSetSetIllumina):
Object instantiation, used by new; not to be called directly by the user.
validObject(ExpressionSetSetIllumina):
Validity-checking method, ensuring that call, callProbability, G, and R are members of assayData. checkValidity(ExpressionSetSetIllumina) imposes this validity check, and the validity checks of Biobase:eSet.
show(ExpressionSetSetIllumina)
See eSet
dim(ExpressionSetSetIllumina), ncol
See eSet
ExpressionSetSetIllumina[(index):
See eSet
ExpressionSetSetIllumina$, ExpressionSetSetIllumina$<-
See eSet

Author(s)

Mark Dunning, based on Biobase eSet class

See Also

eSet


[Package beadarray version 1.10.0 Index]