limmaAnalysis: Differential Expression analysis.

In baba-beda/morpheusR: Visual and interactive gene expression analysis

Differential Expression analysis.

Description

limmaAnalysis performs differential expression analysis from limma package and returns a ProtoBuf-serialized resulting de-matrix.

Usage

limmaAnalysis(
  es,
  fieldValues,
  version = "One-factor design",
  contrast = list("Comparison", "Target", "Reference"),
  designData = NULL
)

Arguments

es	ExpressionSet object. It should be normalized for more accurate analysis.
fieldValues	Vector of comparison values, mapping categories' names to columns/samples
version	name of the limma analysis implementation. Should be "One-factor design" or "Advanced design"
contrast	a character vector with exactly three elements: the name of a factor in the design formula, the name of the numerator level for the fold change, and the name of the denominator level for the fold change
designData	data.frame with design matrix

Value

Name of the file containing serialized de-matrix.

Examples

## Not run: 
data(es)
limmaAnalysis(es, fieldValues = c("A", "A", "A", "B", "B"))

## End(Not run)

baba-beda/morpheusR documentation built on Oct. 10, 2024, 1:35 a.m.