NormiR {ExiMiR} | R Documentation

## ExiMiR high-level function for miRNA raw data normalization.

### Description

This function applies a standard raw data normalization pipeline (i.e. background correction, normalization, PM correction if needed, and summarization) on the input `AffyBatch` object and returns the result in an `ExpressionSet` object.

The methods supported by `NormiR` for the background correction are provided by the `affy` or `limma` packages, depending on whether the input `AffyBatch` object has been created with `ReadAffy` or `ReadExi`/`createAB`, respectively.

By default, it applies the spike-in probe-based method for the second step of normalization. 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.

The next step of PM correction is enabled only when numerical values are available for the MM probes of the input `AffyBatch` object. In this case the methods proposed by `NormiR` are provided by the `affy` package.

The methods supported by `NormiR` for the last step of summarization are also provided by the `affy` package. They do not depend on how the input `AffyBatch` object has been created.

### Usage

    NormiR(abatch,
           # background correction
           bg.correct=TRUE,
           bgcorrect.method='auto',
           bgcorrect.param=list(),
           # normalize
           normalize=TRUE,
           normalize.method='spikein',
           normalize.param=list(),
           # pm correction (enabled only when MM-values are available)
           pmcorrect.method='pmonly',
           pmcorrect.param=list(),
           # expression values
           summary.method='medianpolish',
           summary.param=list(),
           summary.subset=NULL,
           # misc.
           verbose=FALSE,
           ...)

### Arguments

`abatch` | An `AffyBatch` object.
`bg.correct` | Logical. Default is `TRUE`: the background correction step will be performed.
`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.
`normalize` | Logical. Default is `TRUE`: the normalization step will be performed.
`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 `NormiR` 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, `NormiR` uses the probes annotated as "spike-in" by Exiqon or Affymetrix.
`pmcorrect.method` | Character vector. It contains the name of the PM correction method, which is enabled only when numerical values are available for the MM probes of the input `AffyBatch` object. Running `NormiR.pmcorrect.methods(abatch)` indicates which other methods can be chosen instead of the default one `pmonly`.
`pmcorrect.param` | A `R` list of optional parameters for the selected `pmcorrect.method`, as specified in the documentation of the original function `pmcorrect` function of the `affy` package.
`summary.method` | Character vector. It contains the name of the summarization method. Running `NormiR.summary.methods()` indicates which other methods can be chosen instead of the default one `medianpolish`.
`summary.param` | A `R` list of optional parameters for the selected `summary.method`, as specified in the documentation of the original `AffyBatch` method `computeExprSet` contained in the `affy` package.
`summary.subset` | A `R` list of probe set identifiers. When set to its default `NULL` value, the summarized expression values are computed for all probe sets available on the array.
`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 `ExpressionSet` object containing the normalized expression data.

### Author(s)

Sylvain Gubian, Alain Sewer, PMP SA

### See Also

`bg.correct.miR`, `NormiR.bgcorrect.methods`, `norm.miR`, `NormiR.normalize.methods`, `NormiR.spikein.args`, `NormiR.pmcorrect.methods`, `summarize.miR`, `NormiR.summary.methods`.

### Examples

    data(galenv)
    data(GSE20122)
    eset.spike <- NormiR(GSE20122,
                         bg.correct=FALSE,
                         normalize.method='spikein',
                         summary.method='medianpolish')

[Package ExiMiR version 2.28.0 Index]