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],
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.
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:AssayData
phenoData
:eSet
experimentData
:eSet
annotation
:eSet
featureData
: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)
,QCInfo(ExpressionSetIllumina,list)<-
QC
in the AssayData
slot.object[(index)
:combine(ExpressionSetIllumina,ExpressionSetIllumina)
:union
-like
combination in both dimensions of ExpressionSetIllumina objectsshow(ExpressionSetSetIllumina)
eSet
Derived from eSet
:
sampleNames(ExpressionSetSetIllumina)
and sampleNames(ExpressionSetSetIllumina)<-
:eSet
featureNames(ExpressionSetSetIllumina)
, featureNames(ExpressionSetSetIllumina, value)<-
:eSet
dims(ExpressionSetSetIllumina)
:eSet
phenoData(ExpressionSetSetIllumina)
, phenoData(ExpressionSetSetIllumina,value)<-
:eSet
varLabels(ExpressionSetSetIllumina)
, varLabels(ExpressionSetSetIllumina, value)<-
:eSet
varMetadata(ExpressionSetSetIllumina)
, varMetadata(ExpressionSetSetIllumina,value)<-
:eSet
pData(ExpressionSetSetIllumina)
, pData(ExpressionSetSetIllumina,value)<-
:eSet
varMetadata(ExpressionSetSetIllumina)
, varMetadata(ExpressionSetSetIllumina,value)
eSet
experimentData(ExpressionSetSetIllumina)
,experimentData(ExpressionSetSetIllumina,value)<-
:eSet
annotation(ExpressionSetSetIllumina)
, annotation(ExpressionSetSetIllumina,value)<-
eSet
storageMode(eSet)
, storageMode(eSet,character)<-
:eSet
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)
eSet
dim(ExpressionSetSetIllumina)
, ncol
eSet
ExpressionSetSetIllumina[(index)
:eSet
ExpressionSetSetIllumina$
, ExpressionSetSetIllumina$<-
eSet
Mark Dunning, based on Biobase eSet class