R: ExiMiR low-level function for background correction

bg.correct.miR {ExiMiR}

R Documentation

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.

Details

See accompanying vignette.

Value

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

Author(s)

Sylvain.Gubian, Alain Sewer, PMP SA

Examples

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

[Package ExiMiR version 2.29.1 Index]