findBeadStatus {beadarray}R Documentation

Find Outliers

Description

Function finds all beads which are outliers for a given bead type

Usage

findBeadStatus(BLData, probes, array, log=FALSE, n=3, outputValid = FALSE, intProbeID = NULL, ignoreList=NULL, probeIndex=NULL, startSearch=1)

Arguments

BLData BeadLevelList object containing bead level data
probes numeric vector for the ProbeIDs of the bead type we want to find outliers for
array numeric value for the array we want to find outliers on
log if TRUE the log2 intensities of each bead will be used to find outliers. Otherwise un-logged data is used
n numeric value defining a cut-off of 'n' median absolute deviations from the mean to determine outliers. The default value is 3
outputValid if TRUE the IDs of beads which are not outliers will be output
intProbeID BLData$ProbeID coerced to vector of integers. Never change this, for internal use only
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
probeIndex parameter for internal use only
startSearch integer specify where to start searching for a particular ProbeID

Details

The intensities of each bead with ProbeID 'probe' on the specified array are found and if the 'log' parameter is set to true we do a log2 transformation on the set of values.

The mean and median absolute deviation of all the bead intensities are then calculated. Outliers are beads which have intensity more than 'n' median absolute deviations from the mean.

The default setting for the function is the method used by Illumina of un-logged intensities and 'n' = 3.

Any beads which have intensity NA are also counted as outliers

The function returns only the outliers for a bead type unless the outputValid parameter is specified.

Value

List of of row indices relating to the BeadLevelList dividing the beads of this bead type into two categories.

valid valid beads
outliers beads which are calculated as outliers

Author(s)

Mark Dunning

See Also

findAllOutliers

Examples


data(BLData)

findBeadStatus(BLData, 2, 1)

findBeadStatus(BLData, 2, 1, log=TRUE)

##Methods may not always agree

findBeadStatus(BLData, 6140, 1)

findBeadStatus(BLData, 6140, 1, log=TRUE)

##Increasing value of n selects less outliers

findBeadStatus(BLData, 6140, 1, n=4)

findBeadStatus(BLData, 6140, 1, log=TRUE, n=4)


[Package beadarray version 1.0.0 Index]