designMatrix-deprecated {limma}R Documentation

Construct Design Matrix

Description

Construct design matrix from RNA target information.

Usage

designMatrix(targets, parameters, ref, verbose=TRUE)

Arguments

targets matrix or data.frame with columns Cy3 and Cy5 specifying which RNA was hybridized to each array
parameters matrix specifying contrasts between RNA samples which should correspond to regression coefficients. Row names should correspond to unique RNA sample names found in targets.
ref character string giving name of common reference RNA if such exists. Exactly one argument of parameters or ref should be specified.
verbose logical, if TRUE then unique names found in targets will be printed to standard output

Details

This function is intended to produce a design matrix for use in functions lmFit etc for two-color microarray experiments.

Value

designMatrix produces a design matrix with row names as in targets and column names as in parameters.
uniqueTargets produces a character vector of unique target names from the columns Cy3 and Cy5 of targets.

Author(s)

Gordon Smyth

See Also

model.matrix in the base package.

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


[Package limma version 1.6.7 Index]