limmaAnalysis: Perform a limma analysis on expression data.

In birta: Bayesian Inference of Regulation of Transcriptional Activity

Description

Needed for the parameterization of the model as well as the Fisher (pre-)test.

Usage

limmaAnalysis(dat, design, contrasts)

Arguments

dat	A matrix or ExpressionSet containing the expression values.
design	A design matrix.
contrasts	Contrast for the linear model.

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.
design	The design used.
contrast	The contrasts used.

Author(s)

Benedikt Zacher ([e-mail]), Holger Frohlich

References

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

See Also

lmFit, topTable

Examples

data(humanSim)
design = model.matrix(~0+factor(c(rep("control", 5), rep("treated", 5))))
colnames(design) = c("control", "treated")
contrasts = "treated - control"
limmamRNA = limmaAnalysis(sim$dat.mRNA, design, contrasts)

birta documentation built on April 28, 2020, 7:27 p.m.