RGList-class {limma} | R Documentation |
A simple list-based class for storing red and green channel foreground and background intensities for a batch of spotted microarrays.
RGList
objects are normally created by read.maimages
.
RGList
objects can be created by new("RGList",RG)
where RG
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 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 |
Optional components include
weights : | numeric matric 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 PrintLayout. |
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. |
All of the matrices should have the same dimensions.
The row dimension of targets
should match the column dimension of the matrices.
This class inherits directly from class list
so any operation appropriate for lists will work on objects of this class.
In addition, RGList
objects can be subsetted, combined and merged.
RGList
objects will return dimensions and hence functions such as dim
, nrow
and ncol
are defined.
RGLists
also inherit a show
method from the virtual class LargeDataObject
, which means that RGLists
will print in a compact way.
RGList
objects can be converted to exprSet2
objects by as(RG,"exprSet2")
.
Other functions in LIMMA which operate on RGList
objects include
normalizeBetweenArrays
,
normalizeForPrintorder
,
normalizeWithinArrays
.
Gordon Smyth
2.Classes gives an overview of all the classes defined by this package.
marrayRaw-class
is the corresponding class in the marrayClasses package.