getArrayData {beadarray} | R Documentation

## Get raw data from a BeadLevelList object

### Description

Retrieves the raw bead data from a `BeadLevelList` object for a given strip/array.

### Usage

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

### Arguments

`BLData` | `BeadLevelList`
`what` | character string specifying the values to retrieve. Possibilities are `"ProbeID"`, `"GrnX"`, `"GrnY"`, `"G"`, `"Gb"` for single channel data and `"R"`, `"Rb"`, `"residR"`, `"residG"`, `"M"` (log-ratios) `"residM"`, `"A"` (average log-intensities) and `"beta"` (=R/(R+G)) for two-colour data
`array` | integer specifying the strip/array to use
`log` | if TRUE log2 of the raw intensities are returned (ignored if `what="beta"`)
`method` | character string specifying the summarisation method to use in `createBeadSummaryData` (see help page for further details). Only used when `what="residR"`, `"residG"` or `"residM"`.
`n` | numeric value specifying the number of median absolute deviations (MADs) from the median to use as a cut-off for outliers. Only used when `what="residR"`, `"residG"` or `"residM"` and `method="illumina"`.
`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

`getArrayData` retrieves the raw bead data from a given array. The data is either extracted from a `BeadLevelList` object (e.g. `"ProbeID"`, `"GrnX"`, `"GrnY"`, `"G"`, `"Gb"`, `"R"` and `"Rb"` or calculated from these values (e.g. `"residR"`, `"residG"`, `"M"`, `"residM"`, `"A"` or `"beta"`). When `log=TRUE`, intensity data is returned on the log2 scale.

### Value

A vector containing the raw bead data (or residuals) for a particular array.

### Author(s)

Matt Ritchie

### Examples

    data(BLData)
    summary(getArrayData(BLData))

[Package beadarray version 1.12.1 Index]