LumiBatch-class {lumi} | R Documentation |
This is a class representation for Illumina microarray data. It extends ExpressionSet
.
Directly extends class ExpressionSet
.
new('LumiBatch',
exprs = [matrix],
se.exprs = [matrix],
beadNum = [matrix],
detection = [matrix],
phenoData = [AnnotatedDataFrame],
history = [data.frame],
...)
LumiBatch
instances are usually created through
new("LumiBatch", ...)
. The arguments to new
should include exprs
and se.exprs
, others can be
missing, in which case they are assigned default values.
Objects can be created using the function lumiR
.
Slot specific to LumiBatch
:
history
:summary
:
Slots inherited from ExpressionSet
:
assayData
\bf exprs
(contains gene expression level, which is the mean of its bead replicates.),
\bf se.exprs
(contains gene expression standard error, which is the standard error of its bead replicates.),
\bf beadNum
(records the number of beads for the gene.),
\bf detection
(records the detectability of the gene. The number is from [0,1]. Usually > 0.99 indicates good detection.).
For more details of assayData
, please see ExpressionSet
phenoData
:eSet
experimentData
:eSet
annotation
:eSet
Class-specific methods:
se.exprs(LumiBatch)
, se.exprs(LumiBatch,matrix)<-
:se.exprs
in the AssayData-class
slot.beadNum(LumiBatch)
, beadNum(LumiBatch,matrix)<-
:beadNum
in the AssayData-class
slot.detection(LumiBatch)
, detection(LumiBatch,matrix)<-
:detection
in the AssayData-class
slot.getHistory(LumiBatch)
:LumiBatch
object.
Derived from ExpressionSet
(For the directly inherited methods,
please see ExpressionSet
and eSet
):
combine(LumiBatch,missing)
:history
slot. See eSet
exprs(LumiBatch)
, exprs(LumiBatch,matrix)<-
:exprs
in the AssayData-class
slot.object[(i,j)
:
Standard generic methods (For the directly inherited methods,
please see ExpressionSet
and eSet
):
initialize(LumiBatch)
:new
; not to be called directly by the user.validObject(LumiBatch)
:exprs
and se.exprs
is a member of assayData
. Other validity check is the same as checkValidity(ExpressionSet)
.show(LumiBatch)
LumiBatch
object.Pan Du, Simon Lin
lumiR
, lumiT
, lumiN
,
boxplot-methods
, pairs-methods
, MAplot-methods
## load example data data(example.lumi) ## show the summary of the data # summary(example.lumi) example.lumi ## get express matrix temp <- exprs(example.lumi) ## get a subset temp <- example.lumi[,1] ## retrieve the first sample ## get the probe id featureNames(example.lumi)[1:3] ## combine LumiBatch objects temp <- combine(example.lumi[,1], example.lumi[,3]) temp