limmaAnalysis {phantasus}R Documentation

Differential Expression analysis.

Description

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

Usage

limmaAnalysis(es, rows = c(), columns = c(), fieldValues)

Arguments

es

ExpressionSet object. It should be normalized for more accurate analysis.

rows

Vector of specified rows' indices (optional).

columns

Vector of specified columns' indices (optional).

fieldValues

Vector of comparison values, mapping categories' names to columns/samples (must be equal length with columns' vector if specified).

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)

[Package phantasus version 1.0.2 Index]