Class to Contain and Describe High-Throughput Expression Level Assays with Spike-in Data

Description

This is a class representation for spike-in expression data. SpikeInExpressionSet class is derived from ExpressionSet, and requires a matrix names exprs and a matrix named spikeIn.

Extends

Extends class ExpressionSet.

Creating Objects

createSpikeInExpressionSet(exprs, spikeIn, ...)

new("SpikeInExpressionSet", phenoData = new("AnnotatedDataFrame"), featureData = new("AnnotatedDataFrame"), experimentData = new("MIAME"), annotation = character(0), exprs = new("matrix"), spikeIn = new("matrix"))

This creates a SpikeInExpressionSet with assayData implicitly created to contain exprs and spikeIn. Additional named matrix arguments with the same dimensions as exprs are added to assayData; the row and column names of these additional matrices should match those of exprs and spikeIn.

new("SpikeInExpressionSet", assayData = assayDataNew(exprs=new("matrix"),spikeIn=new("matrix")), phenoData = new("AnnotatedDataFrame"), featureData = new("AnnotatedDataFrame"), experimentData = new("MIAME"), annotation = character(0),

This creates a SpikeInExpressionSet with assayData provided explicitly. In this form, the only required named argument is assayData.

Slots

Inherited from ExpressionSet:

assayData:

Contains matrices with equal dimensions, and with column number equal to nrow(phenoData). assayData must contain a matrix exprs and a matrix spikeIn with rows representing features and columns representing samples.

phenoData:

See eSet

annotation

See eSet

featureData

See eSet

experimentData:

See eSet

Methods

Class-specific methods:

spikeIn(SpikeInExpressionSet), spikeIn(SpikeInExpressionSet)<-

Access and set elements named spikeIn in the AssayData-class slot.

spkSplit(SpikeInExpressionSet)

creates two SpikeInExpressionSet objects – one with the spike-in probes and one with the non-spike-in probes.

For derived methods (see ExpressionSet).

See Also

eSet-class, ExpressionSet-class.

Examples

# create an instance of SpikeInExpressionSet
new("SpikeInExpressionSet")

new("SpikeInExpressionSet", exprs=matrix(runif(1000), nrow=100), spikeIn=matrix(rep(1:10,100), nrow=100))

# class specific methods
data(affy)
affySpikes <- spikeIn(affy)
affySplit <- spkSplit(affy)