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 1.10.0 Index]