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, what="G")
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 |
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.
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.
Mark Dunning
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))