SpikeList-class: Class "SpikeList" - Spike Intensity and Concentration List
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. References
the limma package