norm.miR: ExiMiR low-level function for miRNA raw data normalization.

Description

This function performs low-level normalization on an AffyBatch object and returns the result in a new AffyBatch object.

By default, it applies the spike-in probe-based normalization method. In case the spike-in probe-based method cannot be applied, a median normalization is executed instead. Several options allow however to force the execution of the spike-in probe-based normalization and to fine-tune the resulting correction functions.

Usage

norm.miR(abatch, normalize.method="spikein", normalize.param=list(), verbose=TRUE,
	 ...)

Arguments

abatch

An AffyBatch object.

normalize.method

Character vector. It contains the name of normalization method. By default, the spikein method is used. Running NormiR.normalize.methods(abatch) indicates which other methods can be chosen, depending on the raw data contained in the abatch object.

normalize.param

A R list of the arguments that are used to control the spikein normalization. Running NormiR.spikein.args() provides a complete list of all the tunable parameters supported by norm.miR and explained below.

figures.output: Character vector. By default, display is used. Figures are shown to the screen. Using file generates the figures in PDF format in the working directory.
min.corr: Numeric. Default value is 0.5. Minimal allowed value for the average of the off-diagonal elements of the Pearson correlation matrix of the spike-in probeset intensities across the arrays.
loess.span: Numeric. Default value is -1, which corresponds to a loess smoothing neighbourhood spanning a fraction 3/(number of spike-in probesets) of the total number of points. Other positive values are allowed, see the span argument of the R loess function
extrap.points: Numeric. Default value is 2. The number of spike-in probesets used in the high-intensity extrapolation of the normalization correction function.
extrap.method: Character vector. Default value is mean. The method used for the high-intensity extrapolation of the normalization correction function.
force.zero: Logical. Default value is FALSE. If TRUE, it forces the normalization correction functions to have zero values at the lower end of the probe intensity range.
cover.ext: Numeric. Default value is 1/2. Minimal allowed relative coverage of the spike-in probesets intensities. It is computed as the ratio between the intensity range covered by the spike-in probes and the one covered by all probes on the array.
cover.int: Numeric. Default value is 1/3. Maximal allowed relative intensity interval between two consecutive spike-in probesets. It is computed as the largest intensity difference between two consecutive spike-in probesets divided by the overall probe intensity range.
verbose: Logical. Default is TRUE; some details are provided on the console.
max.log2span: Numeric. Default value is 1. Gives the maximal (log2) intensity interval allowed for the probes belonging to one spike-in probeset.
probeset.list: Vector of probes names that will be used as the "spike-in probes". By default, norm.miR uses the probes annotated as "spike-in" by Exiqon or Affymetrix.

verbose

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

...

Any additional argument. Used for backward compatibility.

Value

An AffyBatch object containing the normalized (but not summarized) expression data.

Details

See accompanying vignette.

Examples

Run this code

data(galenv)
data(GSE20122)
GSE20122.normalized <- norm.miR(GSE20122,
                                normalize.param=list(figures.show=FALSE)) 
# Apply the affy method hist on the generated AffyBatch object GSE20122.normalized
layout(matrix(c(1,2), 1, 2, byrow = TRUE))
hist(GSE20122)
hist(GSE20122.normalized)
layout(1)