limmaAnalysis {birte} | R Documentation

## Simple limma analysis on expression data with one contrast.

### Description

This is a convenience function, which can be used to perform a limma analysis with one contrast. Subsequently results may be passed to `birteLimma`

### Usage

    limmaAnalysis(dat, design=NULL, contrast)

### Arguments

`dat` | A matrix or ExpressionSet containing the expression values.
`design` | A design matrix. If no design matrix is provided, the method tries to infer a design matrix by taking column names as a factor. That means the design matrix is constructed according to ~0 + factor(colnames(dat).
`contrast` | Contrast for the linear model. Currently only one contrast is supported. If more contrasts are desired separate biRte analyses should be run for each of them.

### Value

Returns a list containing the following entries:

`pvalue.tab` | Containing the result of the topTable function from limma.
`lm.fit` | Linear fit to the model, i.e. output of function 'eBayes'.
`design` | The design used.
`contrast` | The contrasts used.

### Author(s)

Holger Froehlich

### References

G. K. Smyth. Limma : Linear Models for Microarray Data. Bioinformatics, (2005):397-420.

### Examples

    # see birte.run

[Package birte version 1.20.0 Index]