marrayFit-class {stepNorm}R Documentation

Class "marrayFit", storing parameters and results of post-normalization cDNA microarray data

Description

A simple list-based class for the storage of parameters and results of normalization of cDNA microarray data.

Creating Objects from the Class

Objects can be created by calls of the form new('marrayFit', fit) where fit is a list. Objects of marrayFit in the StepNorm package are typically created by functions fitWithin and fit2DWithin.

List Components

This class contains no slots, but objects should contain the following list components:

varfun
: A character vector of names of predictor variables.
x
: A numeric matrix of predictor variables.
y
: A numeric matrix of repsonses.
residuals
: A numeric matrix of normalized values (typically log ratios (M))
.
fitted
: A numeric matrix of the fitted values.
enp
: The equivalent number of parameters; see loess.
df.residual
: The residual degrees of freedom.
fun
: A character string indicating the name of the function used for normalization.

Methods

This class inherits directly from class list so any operation appropriate for lists will work on objects of this class.

Author(s)

Yuanyuan Xiao, yxiao@itsa.ucsf.edu,
Jean Yee Hwa Yang, jean@biostat.ucsf.edu

See Also

fitWithin, fit2DWithin.

Examples


## load in swirl data
data(swirl)

## median normalization for the first slide of the swirl data
medWithin <- fitWithin(fun="medfit")
## medFit is an object of class marrayFit
medFit <- medWithin(swirl[,1])
## normalized ratios is stored in:
norm.M <- medFit$residuals 

[Package stepNorm version 1.0.2 Index]