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.

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