ParameterList-class {CALIB} | R Documentation |
A simple list-based class for storing all the model parameters of a batch of microarray.
Objects can be created by calls of the form new("ParameterList", parameter)
where parameter is a list. In the CALIB package, ParameterList objects are
normally generated by function estimateParameter
.
Objects should contain the following list components:
MuS
:Ka
:P1
:P2
:SigmaA
:SigmaM
:SigmaS
:SpotError
:Method
:ErrorModel
:log normal
distribution. "N" means spot
capacity follows normal
distribution.genes
:See reference for more detailed explaination for these list components.
Class "list"
, from data part.
Class "vector"
, by class "list"
.
This class inherits directly from class List. However since it represents the parameters
of the calibration model for arrays, it makes on sense to run functions like dim
,
dimnames
,or merge
on this class.
Therefore, only some operations appropriate for list will work on objects of this class.
ParameterList objects can be cbind
and show
in a compact way.
ParameterList objects are used on functions such as normalizeData
or on some other data visualization functions like plotSpikeHI
in the CALIB package.
Hui Zhao
Engelen, K., Naudts, B., DeMoor, B., Marchal, K. (2006) A calibration method for estimating absolute expression levels from microarray data. Bioinformatics 22: 1251-1258.