Spot-class


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


classes

data

genArise is an easy to use tool for dual color microarray
data. Its GUI-Tk based environment let any non-experienced
user performs a basic, but not simple, data analysis just
following a wizard. In addition it provides some tools for the
developer.

IFC Development Team

genArise

Microarray Analysis tool

Spot-class function

Objects can be created by calls of the form <code>new("Spot",spot)</code> where <code>spot</code> is a list.
Objects are normally created by <code><a rd-options="" href="/link/read.spot?package=genArise&version=1.48.0" data-mini-rdoc="genArise::read.spot">read.spot</a></code>.

Creating Objects from the Class

This class contains no slots (other than <code>.Data</code>), but objects should contain the following list components:
<table><tr><td>
  <code>Cy5</code>:</td>
</tr><tr><td> numeric matrix containing the red (cy5) foreground
  intensities. Rows correspond to spots and columns to arrays.</td>
</tr><tr><td>
  <code>Cy3</code>:</td>
</tr><tr><td> numeric matrix containing the green (cy3) foreground intensities.</td>
</tr><tr><td>
  <code>BgCy5</code>:</td>
</tr><tr><td> numeric matrix containing the red (cy5) background intensities.</td>
</tr><tr><td>
  <code>BgCy3</code>:</td>
</tr><tr><td> numeric matrix containing the green background intensities.</td>
</tr></table>
All of these matrices should have the same dimensions.

Slots/List Components

This class inherits directly from class <code>list</code> so any operation appropriate for lists will work on objects of this class.

Methods

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

Spot-class: Spot - class

Description

Arguments

Creating Objects from the Class

Slots/List Components

Methods