# 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

1 | ```
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

1 | ```
# see birte.run
``` |