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 2.34.0
Index]