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)