getArrayData {beadarray}R Documentation

Gets the raw data from a BeadLevelList object

Description

Retrieves the per bead data from a BeadLevelList object for a given 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" or "A" (average log-intensities) for two-colour data
array numeric value giving the array we are interested in
log if TRUE log2 of the raw intensities are returned
method chracter string specifying the summarisation method to use in createBeadSummaryData (see help page for further details). Only used when what="residR", "residG" or "residM".
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".
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 per bead data from a given array. The data is either stored in BeadLevelList object (e.g. "ProbeID", "GrnX", "GrnY", "G", "Gb", "R" and "Rb" or calculated from these values (e.g. "residR", "residG", "M", "residM" or "A"). 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 1.6.0 Index]