outlierPlot {beadarray} | R Documentation |
Diagnostic function that reports how many outliers are found on a specific array on a chip. We take advantage of the segmental structure of the array and break-down the number of outliers into 9 sections.
outlierPlot(BLData, array = array, log = FALSE, plot = FALSE)
BLData |
A BeadLevelList object containing the bead-level data for an Illumina experiment |
array |
The number of the array of interest |
log |
if TRUE calculate outliers on the log2 scale. If FALSE calculate outliers on the original scale |
plot |
if TRUE a diagnostic plot will be produced, otherwise only the numbers of outliers will be returned. |
The number of outliers are computed for the whole array using the Illumina default method that specifies a cut-off of 3 MADs from the median on either the log2 or original scale. These outliers are then split into 9 different sections on the array (the separation between these sections can usually be seen in the plots).
Mark Dunning