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
:G
:Rb
:Gb
:RArea
:GArea
:Optional components include:
weights
:printer
:read.rg
.genes
:targets
:other
: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 merged
. 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.