beadResids {beadarray} | R Documentation |
Retrieves the per bead data stored in a BeadLevelList
object
for a given array. In the case of the log-ratios or average
log-intensities, these values are calculated for each bead.
beadResids(BLData, what="G", array=1, log=TRUE, method="illumina", n=3, trim=0.05)
BLData |
BeadLevelList |
what |
character string specifying which intensities to obtain.
Possibilities are "G" (single channel data) and "R"
(two-colour data) |
array |
numeric value giving the array we are interested in |
log |
if TRUE then use log2 intensities of each bead |
method |
chracter string specifying the summarisation method
(see help page for createBeadSummaryData for further details). |
n |
use n median absolute deviations from the median as a
cut-off for outliers. Only used when what="residR" , "residG"
or "residM" and method="illumina" (see
createBeadSummaryData help page for further details). |
trim |
fraction of intensities to remove from the bead summary
calculations when method="trim" , or the fraction of
intensities to set to the trim and 1-trim percentile
intensities when method="winsorize" . Default value is 0.05.
Only used when what="residR" , "residG" or "residM" . |
Calculates the residuals, i.e. the differences between the summary
values obtained from createBeadSummaryData
and the individual
values for each bead.
A vector containing the residual values.
Matt Ritchie
data(BLData) summary(beadResids(BLData, log=TRUE))