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.

controlData:

a data.frame with first two columns as "controlType" and "ProbeID". The rest columns are the control probe expression amplitudes for individual samples.

QC:

a the quality control information of the LumiBatch object, returned by lumiQ function.

Slots inherited from ExpressionSet:

assayData

contains equal dimensional matrices: exprs (contains gene expression level, which is the mean of its bead replicates.), se.exprs (contains gene expression standard error, which is the standard error of its bead replicates.), beadNum (records the number of beads for the probe.), detection (records the detection p-value of the probe. The number is from [0,1]. By default, < 0.01 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)<-:

Access and set elements named beadNum in the AssayData-class slot. Use "beadNum(LumiBatch) <- NULL" to remove the beadNum element.

detection(LumiBatch), detection(LumiBatch)<-:

Access and set elements named detection in the AssayData-class slot. Use "detection(LumiBatch) <- NULL" to remove the detection element.

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

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## load example data
data(example.lumi)

## show the summary of the data
# summary(example.lumi)
example.lumi	

## get expression 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

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