crosshybMAplot {crosshybDetector}R Documentation

MA-plot

Description

Creates an MA-plot with color coding for corruptor and corrupted probes.

Usage

crosshybMAplot(m, a, subset, badProbes, arrayName, doPlot = FALSE)

Arguments

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

Details

An MA-plot is a plot of log-intensity ratios (M-values) versus log-intensity averages (A-values)

Value

If doPlot is FALSE a plot is created on the current graphics device. If doPlot is TRUE the plot is only written to file.

Author(s)

Paolo Uva

See Also

extractBadProbes

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, 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) 

[Package crosshybDetector version 1.0.4 Index]