| getArrayData {beadarray} | R Documentation |
Retrieves the per bead data from a BeadLevelList object
for a given array.
getArrayData(BLData, what="G", array=1,log=TRUE, method="illumina", n=3, trim=0.05)
BLData |
BeadLevelList |
what |
character string specifying the values to retrieve.
Possibilities are "ProbeID", "GrnX", "GrnY",
"G", "Gb" for single channel data and "R",
"Rb", "residR", "residG", "M" (log-ratios)
"residM" or "A" (average log-intensities) for
two-colour data |
array |
numeric value giving the array we are interested in |
log |
if TRUE log2 of the raw intensities are returned |
method |
chracter string specifying the summarisation method to
use in createBeadSummaryData (see help page for further
details). Only used when what="residR", "residG"
or "residM". |
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". |
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". |
getArrayData retrieves the raw per bead data from a given
array. The data is either stored in BeadLevelList object
(e.g. "ProbeID", "GrnX", "GrnY", "G",
"Gb", "R" and "Rb" or calculated from these
values (e.g. "residR", "residG", "M",
"residM" or "A"). When log=TRUE, intensity
data is returned on the log2 scale.
A vector containing the raw bead data (or residuals) for a particular array.
Matt Ritchie
data(BLData) summary(getArrayData(BLData))