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)