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]