norm.miR {ExiMiR} | R Documentation

## 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.

### Details

See accompanying vignette.

### Value

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

### Author(s)

Sylvain.Gubian, Alain.Sewer, PMP SA

### See Also

`NormiR.normalize.methods`, `NormiR.spikein.args`, `NormiR`.

### Examples

    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)

[Package ExiMiR version 2.28.0 Index]