designMatrix {limma} | R Documentation

## Construct Design Matrix

### Description

Construct a design matrix from the data.frame of target information. Currently only for two color array experiments using a common reference.

### Usage

    designMatrix(targets, ref)

### Arguments

`targets` | data.frame with columns `Cy3` and `Cy5` specifying which RNA was hybridized to each array
`ref` | character string giving name of reference RNA

### Details

There is a need for design matrices for direct two-color design and for single-channel experiments but, this version is only for reference designs.

### Value

The design matrix.

### Author(s)

Gordon Smyth

### See Also

An overview of linear model functions in limma is given by 5.LinearModels.

### Examples

    targets <- data.frame(Cy3=c("Ref","Control","Ref","Treatment"),Cy5=c("Control","Ref","Treatment","Ref"))
    designMatrix(targets, "Ref")

[Package Contents]