| crosshybMAplot {crosshybDetector} | R Documentation |
Creates an MA-plot with color coding for corruptor and corrupted probes.
crosshybMAplot(m, a, subset, badProbes, arrayName, doPlot = FALSE)
m |
a vector containing log2(ratios) |
a |
a vector containing log2(average intensities) |
subset |
the subset of probes to be plotted |
badProbes |
the output of extractBadProbes containing corruptor
and corrupted probes for red and green channels |
arrayName |
the name of the array. Used to create the output file name |
doPlot |
logical, if TRUE writes the plot to file |
An MA-plot is a plot of log-intensity ratios (M-values) versus log-intensity averages (A-values)
If doPlot is FALSE a plot is created on the current graphics device.
If doPlot is TRUE the plot is only written to file.
Paolo Uva
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, probeNameID="Name",
probes="probes", satValue = 65535, maxProbes=100)
## End(Not run)
# ...or load directy crosshyb output
data(crosshyb.out)
# Extract bad probes
badProbes <- extractBadProbes(crosshyb.out, pVal=0.01)
# Loess normalization using only probes
# Use maNorm function from marray package
norm <- maNorm(raw, norm="l", subset=maControls(raw) == "probes")
# MA plot showing corruptor and corrupted probes
crosshybMAplot(m = maM(norm),
a = maA(norm),
subset=maControls(raw) %in% c("probes", "spike"),
badProbes=badProbes,
arrayName="myArray",
doPlot=FALSE)