BeadLevelList-class {beadarray}R Documentation

Class "BeadLevelList"

Description

A simple list-based class for storing red and green channel foreground and background intensities for an Illumina experiment.

Objects from the Class

Objects can be created by calls of the form new("BeadLevelList", G, Gb, x, y, ProbeID, targets), but are usually created by readBeadLevelData.

Slots/List Components

BeadLevelList objects can be created by new("BeadLevelList",BLData) where BLData is a list. Objects of this class contains no slots (other than .Data), but objects should contain the following list components:
R: numeric matrix containing the red (foreground intensities. Rows correspond to spots and columns to arrays.
G: numeric matrix containing the green foreground intensities
Rb: numeric matrix containing the red background intensities
Gb: numeric matrix containing the green background intensities

Methods

show(BeadLevelList)
printing method for BeadLevelList
initialize
signature(.Object = "BeadLevelList")
createBeadSummaryData
Summarise each probe on the array to create an ExpressionSetIlluminaObject
imageplot(BeadLevelList)
An imageplot function for BeadLevelList
findAllOutliers(BeadLevelList)
Find all beads on an array that are outliers for their particular bead type

Author(s)

Mark Dunning

See Also

readBeadLevelData


[Package beadarray version 1.2.2 Index]