limmaAnalysis

A matrix or ExpressionSet containing the expression values.

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).

design

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.

contrast


This is a convenience function, which can be used to perform a limma analysis with one contrast. Subsequently results may be passed to <code><a rd-options="" href="/link/birteLimma?package=birte&version=1.8.1" data-mini-rdoc="birte::birteLimma">birteLimma</a></code>


Expression levels of mRNA molecules are regulated by
different processes, comprising inhibition or activation by
transcription factors and post-transcriptional degradation by
microRNAs. biRte uses regulatory networks of TFs, miRNAs and
possibly other factors, together with mRNA, miRNA and other
available expression data to predict the relative influence of
a regulator on the expression of its target genes. Inference is
done in a Bayesian modeling framework using
Markov-Chain-Monte-Carlo. A special feature is the possibility
for follow-up network reverse engineering between active
regulators.

Holger Froehlich

birte

Bayesian Inference of Regulatory Influence on Expression (biRte)

limmaAnalysis function

This is a convenience function, which can be used to perform a limma analysis with one contrast. Subsequently results may be passed to <code><a href="birteLimma" rd-options="">birteLimma</a></code>

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

Description

Usage

Arguments

Value

References

Examples