outlierPlot {beadarray}R Documentation

Locations of outliers on an Illumina chip

Description

Diagnostic function that reports how many outliers are found on a specific array on a chip. We take advantage of the segmental structure of the array and break-down the number of outliers into 9 sections.

Usage

outlierPlot(BLData, array = array, log = FALSE, plot = FALSE)

Arguments

BLData A BeadLevelList object containing the bead-level data for an Illumina experiment
array The number of the array of interest
log if TRUE calculate outliers on the log2 scale. If FALSE calculate outliers on the original scale
plot if TRUE a diagnostic plot will be produced, otherwise only the numbers of outliers will be returned.

Details

The number of outliers are computed for the whole array using the Illumina default method that specifies a cut-off of 3 MADs from the median on either the log2 or original scale. These outliers are then split into 9 different sections on the array (the separation between these sections can usually be seen in the plots).

Author(s)

Mark Dunning


[Package beadarray version 1.10.0 Index]