RGList_CALIB-class: Red, Green Intensity List - Class

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 for a batch of spotted microarrays. It is a extension of the RGList in the LIMMA package.

Objects from the Class

Objects can be created by calls of the form new("RGList_CALIB", RG), where RG is a list. In the CALIB package, RGList\_CALIB objects are normally generated by read.rg.

List Components

objects should contain the following list components:

R:

numeric matrix containing the red(Cy5) foreground intensities. Rows correspond to spots and columns to arrays.

G:

numeric matrix containing the green(Cy3) foreground intensities.

Rb:

numeric matrix containing the red(Cy5) background intensities.

Gb:

numeric matrix containing the green(Cy3) background intensities.

RArea:

numeric matrix containing the red(Cy5) spot areas.

GArea:

numeric matrix containing the green(Cy3) spot areas.

Optional components include:

weights:

numeric matrix containing relative spot quality weights. Should be non-negative.

printer:

list containing information on the process used to print the spots on the arrays. See read.rg.

genes:

data.frame containing information on the genes spotted on the arrays. Should include a character column Name containing names for the genes or controls.

targets:

data.frame containing information on the target RNA samples. Should include factor or character columns Cy3 and Cy5 specifying which RNA was hybridized to each array.

other:

list containing numeric matrices of other spot-specific information.

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

Extends

Class "list", from data part. Class "LargeDataObject", directly. 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, RGList\_CALIB objects can be subsetted, combined and merge. RGList\_CALIB objects will return dimensions and hence functions such as dim, dimnames, nrow and ncol are defined. RGList\_CALIB also inherit a show method from the virtual class LagerDataObject, which means that RGList\_CALIB objects will print in a compact way.

In the CALIB package, RGList\_CALIB objects are mainly for storing microarray data and they are used to pass microarray data into functions such as estimateParameter or normalizeData.

Author(s)

Hui Zhao

References

RGList in the limma package

See Also

RGList and LargeDataObject in limma packge.

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