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]