bg.correct.miR: ExiMiR low-level function for background correction

Description

This function performs background correction on an AffyBatch object.

The methods supported by bg.correct.miR are provided by the affy or limma packages, depending on whether the input AffyBatch object has been created with ReadAffy or ReadExi/createAB, respectively.

Usage

bg.correct.miR(abatch,
	       bgcorrect.method='auto',
	       bgcorrect.param=list(),
	       verbose=FALSE)

Arguments

abatch

An AffyBatch object.

bgcorrect.method

Character vector. It contains the name of the background correction method. Running NormiR.bgcorrect.methods(abatch) indicates which methods can be used, depending on the raw data contained in the abatch object. The auto option corresponds to the default choice of applying rma for single-channel arrays and normexp for dual-channel arrays.

bgcorrect.param

A R list containing the parameters required by the selected background correction method, as specified in the documentation of the original functions bg.correct of the affy package or backgroundCorrect of the limma package. As an illustration the parameters of the normexp method of the limma package are given below.

normexp.method: Character vector. The variant of the normexp method, matching exactly the argument normexp.method of the backgroundCorrect function.
offset: Numeric value to add to intensities. It matches exactly the argument offset of the backgroundCorrect function.

verbose

Logical. The default value is TRUE. The details of the function execution are displayed on the console.

Value

An AffyBatch object containing the background-corrected raw expression data.

Details

See accompanying vignette.

Examples

Run this code

data(galenv)
data(GSE20122)
NormiR.bgcorrect.methods(GSE20122)
GSE20122.bgcorrected <- bg.correct.miR(GSE20122,
                                       bgcorrect.method='normexp',
                                       bgcorrect.param=list(offset=50))