SpikeList-class: Class "SpikeList" - Spike Intensity and Concentration List

In CALIB: Calibration model for estimating absolute expression levels from microarray data

Description

A simple list-based class for storing red and green channel foreground and background intensities, spot area and concentrations for external control spike on spotted microarray.

Objects from the Class

Objects can be created by calls of the form new("SpikeList", spike) where spike is a list. In the CALIB package, SpikeList objects are normally generated by function read.spike.

List Components

Objects should contain the following list components:

R:

numeric matrix containing the red(Cy5) foreground intensities of all external control spikes on arrays. Rows correspond to spikes and columns to arrays.

G:

numeric matrix containing the green(Cy3) foreground intensities of all external control spikes on arrays.

Rb:

numeric matrix containing the red(Cy5) background intensities of all external control spikes on arrays.

Gb:

numeric matrix containing the green(Cy3) background intensities of all external control spikes on arrays.

RArea:

numeric matrix containing the red(Cy5) spot areas of all external control spikes on arrays.

GArea:

numeric matrix containing the green(Cy3) spot areas of all external control spikes on arrays.

RConc:

numeric matrix containing the red(Cy5) known concentrations of all external control spikes on arrays.

GConc:

numeric matrix containing the green(Cy3) know concentrations of all external control spikes on arrays.

genes:

data.frame containing information on spikes spotted on the arrays. Should include a character column Name containing names for all the spikes.

All of the matrices should have the same dimensions.

Extends

Class "list", from data part. Class "vector", by class "list".

Methods

This class inherits directly from class List, so any operation appropriate for lists will work on objects of this class. In addition, SpikeList objects can be subsetted, combined and merged. SpikeList objects will return dimensions and hence functions such as dim, dimnames, nrow and ncol are defined. Generic method show is applied on SpikeList, so SpikeList will print in a compact way.

SpikeList objects are used on functions such as estimateParameter or on some other data visualization functions like plotSpikeHI in the CALIB package.

Author(s)

Hui Zhao

References

the limma package

See Also

RGList_CALIB.

RGList in limma package.

CALIB documentation built on Oct. 31, 2019, 3:45 a.m.