LumiBatch-class {lumi}R Documentation

Class LumiBatch: contain and describe Illumina microarray data

Description

This is a class representation for Illumina microarray data. It extends ExpressionSet.

Extends

Directly extends class ExpressionSet.

Creating Objects

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.

Slots

Slot specific to LumiBatch:

history:
a data.frame recording the operation history of the LumiBatch object.
summary:
a summary of the LumiBatch object.

Slots inherited from ExpressionSet:

assayData
contains equal dimensional matrices: \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:
See eSet
experimentData:
See eSet
annotation:
See eSet

Methods

Class-specific methods:

se.exprs(LumiBatch), se.exprs(LumiBatch,matrix)<-:
Access and set elements named se.exprs in the AssayData-class slot.
beadNum(LumiBatch), beadNum(LumiBatch,matrix)<-:
Access and set elements named beadNum in the AssayData-class slot.
detection(LumiBatch), detection(LumiBatch,matrix)<-:
Access and set elements named detection in the AssayData-class slot.
getHistory(LumiBatch):
Access the operation history of LumiBatch object.

Derived from ExpressionSet (For the directly inherited methods, please see ExpressionSet and eSet):

combine(LumiBatch,missing):
Combine two LumiBatch objects, including history slot. See eSet
exprs(LumiBatch), exprs(LumiBatch,matrix)<-:
Access and set elements named exprs in the AssayData-class slot.
object[(i,j):
Conduct subsetting of the data in a LumiBatch object

Standard generic methods (For the directly inherited methods, please see ExpressionSet and eSet):

initialize(LumiBatch):
Object instantiation, used by new; not to be called directly by the user.
validObject(LumiBatch):
Validity-checking method, ensuring that exprs and se.exprs is a member of assayData. Other validity check is the same as checkValidity(ExpressionSet).
show(LumiBatch)
A summary of the LumiBatch object.

Author(s)

Pan Du, Simon Lin

See Also

lumiR, lumiT, lumiN, boxplot-methods, pairs-methods, MAplot-methods

Examples

## 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


[Package lumi version 1.4.0 Index]