beadResids {beadarray}R Documentation

Calculates per strip/array bead-level residuals

Description

Calculates the per bead residuals for a given strip/array using data from a BeadLevelList.

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 use in the calculation of residuals. See getArrayData for a list of possibilities
array integer specifying the strip/array to use
log if TRUE then use log2 intensities of each bead
method character string specifying the summarisation method (see help page for createBeadSummaryData for further details).
n numeric value defining a cut-off for the number of median absolute deviations (MADs) from the median to use for determining outliers. The default value is 3. Only used when 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 1.10.0 Index]