findAllOutliers {beadarray} | R Documentation |
Function to find all beads which are outliers for their particular bead type on a given array.
findAllOutliers(BLData, array, log=FALSE, n=3, ignoreList=NULL)
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 |
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.
numeric vector giving a row index from the BeadLevelList for all the beads that are outliers for their bead type.
Mark Dunning and Mike Smith
data(BLData) length(findAllOutliers(BLData, 1)) length(findAllOutliers(BLData, 1, log=TRUE)) length(findAllOutliers(BLData, 1, n=5))