| crosshyb2xls {crosshybDetector} | R Documentation |
This function writes corruptor and corrupted probes to tab-delimited files.
Each file contains the probe names and the corresponding raw (before normalization) foreground and background signals.
crosshyb2xls(raw, array = NULL, parent, children, arrayName,
channel = c("red", "green"), probeNameID = c("ProbeName", "Name"))
raw |
An object of class marrayRaw |
array |
Integer. The array to analyze |
parent |
A vector with the index of the corruptor probes, as returned
by extractBadProbes |
children |
A vector with the index of the corrupted probes, as returned
by extractBadProbes |
arrayName |
The name of the array to analyze. It is used to create the output file names |
channel |
The channel to analyze |
probeNameID |
The slot name of raw containing the probe names.
Probes names are extracted with maInfo(maGnames(raw)[[probeNameID]] |
Write a tab-delimited files for each channel of a dual channel microarray experiment
into the current directory. Each file has four columns:
ProbeNumber, ProbeName, Foreground\_Raw and Background\_Raw
containing respectively the probe number, probe name and the foreground and
background raw signals (before normalization)
Paolo Uva
extractBadProbes, crosshyb, crosshybImage
data(raw)
data(probeSeq)
## Not run:
# Run crosshyb...
# This function will take several minutes to finish
crosshyb.out <- crosshyb(raw, probeSeq, plate=1, numPermut=10000, name="Name",
probes=c("probes", "spike"), satValue = 65535,
maxProbes=100)
## End(Not run)
# ... or load directly crosshyb output
data(crosshyb.out)
# Extract corrupted and corruptor probes
badprobes <- extractBadProbes(crosshyb.out, pVal=0.05)
## Not run:
# Write results for RED channel
if(!length(badprobes$corruptorsR)){
parent <- badprobes$corruptorsR
child <- badprobes$corruptedR
crosshyb2xls(raw, array=1, parent=parent, children=child,
arrayName="myArray", channel="red", probeNameID="Name")
}
## End(Not run)