codPlot {codelink} | R Documentation

## 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.

### Author(s)

Diego Diez

[Package codelink version 1.48.0 Index]