beadResids {beadarray} | R Documentation

## Calculates per array bead-level residuals

### Description

Retrieves the per bead data stored in a `BeadLevelList` object for a given array. In the case of the log-ratios or average log-intensities, these values are calculated for each bead.

### Usage

    beadResids(BLData, what="G", array=1, log=TRUE,
                     method="illumina", n=3, trim=0.05)

### Arguments

`BLData` | `BeadLevelList`
`what` | character string specifying which intensities to obtain. Possibilities are `"G"` (single channel data) and `"R"` (two-colour data)
`array` | numeric value giving the array we are interested in
`log` | if TRUE then use log2 intensities of each bead
`method` | chracter string specifying the summarisation method (see help page for `createBeadSummaryData` for further details).
`n` | use n median absolute deviations from the median as a cut-off for outliers. Only used when `what="residR"`, `"residG"` or `"residM"` and `method="illumina"` (see `createBeadSummaryData` help page for further details).
`trim` | fraction of intensities to remove from the bead summary calculations when `method="trim"`, or the fraction of intensities to set to the `trim` and 1-`trim` percentile intensities when `method="winsorize"`. Default value is 0.05. Only used when `what="residR"`, `"residG"` or `"residM"`.

### Details

Calculates the residuals, i.e. the differences between the summary values obtained from `createBeadSummaryData` and the individual values for each bead.

### Value

A vector containing the residual values.

### Author(s)

Matt Ritchie

### Examples

    data(BLData)
    summary(beadResids(BLData, log=TRUE))

[Package beadarray version 1.6.0 Index]