limmaAnalysis: Simple limma analysis on expression data with one contrast.

In birte: Bayesian Inference of Regulatory Influence on Expression (biRte)

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

birte documentation built on May 2, 2019, 12:32 a.m.