RGList_CALIB-class {CALIB} | R Documentation |
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 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
.
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.
Class "list"
, from data part.
Class "LargeDataObject"
, directly.
Class "vector"
, by class "list"
.
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
.
Hui Zhao
RGList
in the limma package
RGList
and
LargeDataObject
in limma packge.