Diagnostic plots for CodelinkSet object.

Description

This function performs several types of diagnostic plots using information from CodelinkSet objects.

Usage

1
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.

Author(s)

Diego Diez

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