BeadLevelList-class {beadarray}R Documentation

Red, Green Intensity List - class

Description

A simple list-based class for storing red and green channel foreground and background intensities for a batch of spotted microarrays.

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 foreground intensities. Rows correspond to beads and columns to arrays.
Rb: numeric matrix containing the local background intensities
ProbeID: matrix containing the bead type (probe type) for each bead
x: numeric matrix containing the x coordinate for the centre of each bead
y: numeric matrix containing the y coordinate for the centre of each bead

All of the matrices should have the same dimensions. The row dimension of targets should match the column dimension of the matrices.

Methods

This class inherits directly from class list so any operation appropriate for lists will work on objects of this class. In addition, BeadLevelList objects can be subsetted, combined and merged. BeadLevelList objects will return dimensions and hence functions such as dim, nrow and ncol are defined. BeadLevelLists also inherit a show method from the virtual class LargeDataObject, which means that BeadLevelLists will print in a compact way.

Author(s)

Mark Dunning


[Package beadarray version 1.0.0 Index]