beadResids {beadarray} | R Documentation |
Calculates the per bead residuals for a given strip/array using
data from a BeadLevelList
.
beadResids(BLData, what="G", array=1, log=TRUE, method="illumina", n=3, trim=0.05)
BLData |
BeadLevelList |
what |
character string specifying which intensities to use in the
calculation of residuals. See getArrayData for a list of possibilities |
array |
integer specifying the strip/array to use |
log |
if TRUE then use log2 intensities of each bead |
method |
character string specifying the summarisation method
(see help page for createBeadSummaryData for further details). |
n |
numeric value defining a cut-off for the number of
median absolute deviations (MADs) from the median to use for
determining outliers. The default value is 3. Only used when
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))