plotMA {limma} | R Documentation

## MA-Plot

### Description

Creates an MA-plot with color coding for various sort of control spots.

### Usage

    plotMA(MA,array=1,pch=16,status=NULL,
           values=c("gene","blank","buffer","utility","negative","calibration","ratio"),
           col=c("black","yellow","orange","pink","brown","blue","red"),
           cex=c(0.1,0.6,0.6,0.6,0.6,0.6,0.6))

### Arguments

`MA` | list with components `M` containing log-ratios and `A` containing average intensities
`array` | integer giving the array to be plotted. Corresponds to columns of `M` and `A`.
`pch` | vector or list of plotting characters
`status` | character vector giving the control status of each spot on the array. If `NULL` then subsequent arguments are ignored.
`values` | character vector giving unique values of `status` corresponding to control states of interest
`col` | vector of colors, of the same length as `values`
`cex` | numeric vector of the same length as `values` giving sizes for plot symbols

### Details

See `points` for possible values for `pch`, `col` and `cex`.

### Value

A plot is created on the current graphics device.

### Author(s)

Gordon Smyth

### See Also

An overview of diagnostic functions available in LIMMA is given in 6.Diagnostics.

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