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, ignoreList=NULL)

Arguments

BLData an BeadLevelList object containing bead level data
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 from the mean. The default value is 3
ignoreList list of ProbeIDs to be omitted from the averaging procedure. These could be Illumina internal controls which are replicated many thousands of times on arrays

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 mean.

Value

numeric vector giving a row index from the BeadLevelList for all the beads that are outliers for their bead type.

Author(s)

Mark Dunning and Mike Smith

See Also

findBeadStatus

Examples


data(BLData)

length(findAllOutliers(BLData, 1))

length(findAllOutliers(BLData, 1, log=TRUE))

length(findAllOutliers(BLData, 1, n=5))


[Package beadarray version 1.0.0 Index]