fixOutliers {MmPalateMiRNA} | R Documentation

## 'Fix' an `RGList` object with outlying values.

### Description

Imputes outlying values in one of the red foreground, red background, green foreground, or green background matrices of an `RGList` object created from Miltenyi Biotech miRXplore Microarrays. Uses the replicate structure of the array to impute the outlying values. Implicit assumption is that only one of the four replicated values for a probe is an outlying value.

### Usage

    fixOutliers(mat, idx, gene.ids)

### Arguments

`mat` | One of the red foreground (`R`), red background (`Rb`), green foreground (`G`), or green background (`Gb`) matrices in an `RGList` object, which contains outlying values.
`idx` | Index of outlying values, as returned by the `checkOutliers` function. See examples for usage.
`gene.ids` | Vector of gene IDs for each probe. See examples for usage.

### Details

The function is specific to `RGList` objects which were created from Miltenyi Biotech miRXplore Microarrays, since it depends on the replicated structure of that array (probes spotted in quadruplicate) to impute the outlying probe values.

### Value

Returns a matrix with the outlying probe values imputed.

### See Also

`checkOutliers`, `checkMVs`, `fixMVs`

### Examples

    data(PalateData)
    outliers <- checkOutliers(PalateData)
    PalateData$R <- fixOutliers(PalateData$R, outliers$Rout, PalateData$genes$Gene)

[Package MmPalateMiRNA version 1.30.0 Index]