findAllOutliers {beadarray}R Documentation

Find outliers on array

Description

Function to find all beads which are outliers for their particular bead type on a given array.

Usage

findAllOutliers(BLData, array, log=FALSE, n=3, what="G")

Arguments

BLData a BeadLevelList object
array numeric value specifying which array we want to find outliers on
log if TRUE the log2 intensities will be used to calculate outliers
n Specify a cut-off for outliers as n median absolute deviations (MADs) from the median. The default value is 3
what character string specifying which intensities to use. Possibilities are "G", "Gb" for single channel data and "G", "Gb", "R" and "Rb" for two-colour data

Details

We find the outliers for each bead type on the array in turn using the findBeadStatus function and keep a list of the outliers found. By default, outliers for a particular bead type are determined using a 3 MAD cut-off from the median.

Value

numeric vector giving the row indices of BLData (in the range 1 to total number of beads on the array) of all the beads that are outliers for their bead type.

Author(s)

Mark Dunning

See Also

findBeadStatus

Examples

data(BLData)
# how many outliers are there on the original scale?
length(findAllOutliers(BLData, 1))
# how many outliers are there on the log2-scale?
length(findAllOutliers(BLData, 1, log=TRUE)) #
# how many outliers are there using a 4 MAD 
# cut-off from the median?
length(findAllOutliers(BLData, 1, n=4))

[Package beadarray version 1.6.0 Index]