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))