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")

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