crosshyb2xls {crosshybDetector}R Documentation

Write corruptor and corrupted probes to files

Description

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.

Usage

crosshyb2xls(raw, array = NULL, parent, children, arrayName,
             channel = c("red", "green"), probeNameID = c("ProbeName", "Name"))

Arguments

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]]

Value

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)

Author(s)

Paolo Uva

See Also

extractBadProbes, crosshyb, crosshybImage

Examples

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)


[Package crosshybDetector version 1.0.4 Index]