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.