limmaTwoLevels: Wrapper for the limma function for the comparison of two...

In a4Base: Automated Affymetrix Array Analysis Base Package

Description

Wrapper for the limma function for the comparison of two groups (two factor levels)

Usage

limmaTwoLevels(object, group, probe2gene = TRUE)

Arguments

object	object of class ExpressionSet
group	string indicating the variable defining the two groups to be compared
probe2gene	logical; if TRUE Affymetrix probeset IDs are translated into gene symbols; if FALSE no such translation is done

Value

S4 object of class 'limma' with the following two components:

MArrayLM	S4 object of class MArrayLM as returned by the limma function of the limma package
geneSymbols	character vector of gene symbols; this slot is only populated if probe2gene=TRUE (and if the ExpressionSet object is appropriately annotated by addGeneInfo for gene symbols to be extracted)

Note

A 'topTable' method is defined for 'limma' objects.

Author(s)

Tobias Verbeke and Willem Talloen

a4Base documentation built on Nov. 8, 2020, 5:41 p.m.