| ExpressionSetIllumina {beadarray} | R Documentation |
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.
Directly extends class eSet.
new('ExpressionSetIllumina',
phenoData = [AnnotatedDataFrame],
experimentData = [MIAME],
annotation = [character],
exprs = [matrix],
se.exprs = [matrix],
NoBeads = [matrix],
Detection = [matrix],
reporterInfo = [data.frameOrNULL],
...)
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.
Inherited from eSet:
assayData: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:AssayDataphenoData:eSetexperimentData:eSetannotation:eSetreporterInfo:CHR and a MapInfo column for genomic localization Class-specific methods:
exprs(ExpressionSetIllumina), exprs(ExpressionSetIllumina,matrix)<-exprs in the AssayData
slot.se.exprs(ExpressionSetIllumina), se.exprs(ExpressionSetIllumina,matrix)<-se.exprs in the AssayData
slot.NoBeads(ExpressionSetIllumina)NoBeads in the AssayData
slot.Detection(ExpressionSetIllumina)Detection in the AssayData
slot.getVariance(ExpressionSetIllumina)se.exprs and
NoBeads from the AssayData slot.QCInfo(ExpressionSetIllumina)QC in the AssayData
slot.object[(index):combine(ExpressionSetIllumina,ExpressionSetIllumina):union-like
combination in both dimensions of ExpressionSetIllumina objectsshow(ExpressionSetSetIllumina)eSetbackgroundNormalise(ExpressionSetIllumina)QC slot.
Derived from eSet:
sampleNames(ExpressionSetSetIllumina) and sampleNames(ExpressionSetSetIllumina)<-:eSetfeatureNames(ExpressionSetSetIllumina), featureNames(ExpressionSetSetIllumina, value)<-:eSetdims(ExpressionSetSetIllumina):eSetphenoData(ExpressionSetSetIllumina), phenoData(ExpressionSetSetIllumina,value)<-:eSetvarLabels(ExpressionSetSetIllumina), varLabels(ExpressionSetSetIllumina, value)<-:eSetvarMetadata(ExpressionSetSetIllumina), varMetadata(ExpressionSetSetIllumina,value)<-:eSetpData(ExpressionSetSetIllumina), pData(ExpressionSetSetIllumina,value)<-:eSetvarMetadata(ExpressionSetSetIllumina), varMetadata(ExpressionSetSetIllumina,value)eSetexperimentData(ExpressionSetSetIllumina),experimentData(ExpressionSetSetIllumina,value)<-:eSetpubMedIds(ExpressionSetSetIllumina), pubMedIds(ExpressionSetSetIllumina,value)eSetabstract(ExpressionSetSetIllumina):eSetannotation(ExpressionSetSetIllumina), annotation(ExpressionSetSetIllumina,value)<-eSetstorageMode(eSet), storageMode(eSet,character)<-:eSetreporterNames(ExpressionSetSetIllumina), reporterNames(ExpressionSetSetIllumina,value)<-:Standard generic methods:
initialize(ExpressionSetSetIllumina):new; not to be called directly by the user.validObject(ExpressionSetSetIllumina):call, callProbability, G, and R are members of
assayData. checkValidity(ExpressionSetSetIllumina) imposes this
validity check, and the validity checks of Biobase:eSet.show(ExpressionSetSetIllumina)eSetdim(ExpressionSetSetIllumina), ncoleSetExpressionSetSetIllumina[(index):eSetExpressionSetSetIllumina$, ExpressionSetSetIllumina$<-eSetMark Dunning, based on Biobase eSet class