| getArrayData {beadarray} | R Documentation |
Retrieves the raw bead data from a BeadLevelList object
for a given strip/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", "A" (average log-intensities) and "beta"
(=R/(R+G)) for two-colour data |
array |
integer specifying the strip/array to use |
log |
if TRUE log2 of the raw intensities are returned (ignored if what="beta") |
method |
character string specifying the summarisation method to
use in createBeadSummaryData (see help page for further
details). Only used when what="residR", "residG"
or "residM". |
n |
numeric value specifying the number of median absolute deviations (MADs)
from the median to use 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 bead data from a given
array. The data is either extracted from a BeadLevelList object
(e.g. "ProbeID", "GrnX", "GrnY", "G",
"Gb", "R" and "Rb" or calculated from these
values (e.g. "residR", "residG", "M",
"residM", "A" or "beta").
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))