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birta (version 1.16.0)

limmaAnalysis: Perform a limma analysis on expression data.

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.

References

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

See Also

lmFit, topTable

Examples

Run this code
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)

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