findAllOutliers {beadarray} | R Documentation

## Find outliers on array

### Description

Function to find all beads which are outliers for their particular bead type on a given array.

### Usage

    findAllOutliers(BLData, array, log=FALSE, n=3, ignoreList=NULL)

### Arguments

`BLData` | an BeadLevelList object containing bead level data
`array` | numeric value specifying which array we want to find outliers on
`log` | if TRUE the log2 intensities will be used to calculate outliers
`n` | Specify a cut-off for outliers as n median absolute deviations from the mean. The default value is 3
`ignoreList` | list of ProbeIDs to be omitted from the averaging procedure. These could be Illumina internal controls which are replicated many thousands of times on arrays

### Details

We find the outliers for each bead type on the array in turn using the `findBeadStatus` function and keep a list of the outliers found. By default, outliers for a particular bead type are determined using a 3 MAD cut-off from the mean.

### Value

numeric vector giving a row index from the BeadLevelList for all the beads that are outliers for their bead type.

### Author(s)

Mark Dunning and Mike Smith

### See Also

`findBeadStatus`

### Examples

    data(BLData)

    length(findAllOutliers(BLData, 1))

    length(findAllOutliers(BLData, 1, log=TRUE))

    length(findAllOutliers(BLData, 1, n=5))

[Package beadarray version 1.0.0 Index]