codPlot:
Diagnostic plots for CodelinkSet object.
Description
This function performs several types of diagnostic plots using information from CodelinkSet objects.
Usage
codPlot(object, array, what = "ma", ...)
Arguments
object
a CodelinkSet object.
array
The array to use for plotting (by default array=1).
what
the type of plot (by default ma).
...
additional arguments passed to the appropriate functions.
Details
Plot types:
scatter-
Scatter plot of the selected array intensities vs. the median array, or a second array if specified.
ma
MA plot of the selected array intensities vs. the median array, or a second array if specified. In the x-axis the value of A (mean abundance; A = Array1 + Array2) is plotted. In the y-axis the value of M (difference; M = Array1 - Array2) is plotted.
density
The distribution of intensities for each array in the dataset is plotted as a kernel density.
image
If the logical position of the probes in the array are available, this plot produces a pseudoimage of the array. The values of the "intensity", "bg" or "snr" can be selected with the 'signal' parameter (default signal="bg"). Color range can be controled with 'high' and 'low' parameters.