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

### See Also

`NormiR.bgcorrect.methods`, `NormiR`.

### 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]