maDiagnPlots {marray} | R Documentation

## Basic diagnostic plots

### Description

These three functions produce sets of basic diagnostic plots for pre- and post-normalization cDNA microarray data.

### Usage

    maDiagnPlots(mraw, mNorm = NULL, save = TRUE, fname = NULL,
    dev= "png", pch, col, DEBUG = FALSE, ...)

### Arguments

`mraw` | Microarray object of class `"marrayRaw"'. By default, plots are done for the first array in the batch.
`mNorm` | Microarray object of class `"marrayNorm"'. By default, this value is NULL and the function maNorm is call to perform normalization.
`save` | If `TRUE', the figures will be saved to the file named in `fname'.
`fname` | A "character" string naming the output file.
`dev` | A "character" string naming the graphics device.
`pch` | point style for different control samples.
`col` | color code for different control samples.
`DEBUG` | If 'TRUE', debug statements are printed.
`...` | Optional graphical parameters, see `par'.

### Details

`maDiagnPlots` produces plots of pre- and post-normalization cDNA microarray data: color images of log-ratios (M) and log-intensities (A) pre- and post-normalization. MA-plots of pre- and post-normalization log-ratios M. Log foreground to background ratios for both Cy5 and Cy3 channels. Dot plots for replicate control spots.

### Note

This function may not work properly when "save=FALSE".

### Author(s)

Yee Hwa (Jean) Yang

### See Also

`maPlot`, `maImage`, `maBoxplot`

### Examples

    data(swirl)
    ## maDiagnPlots(swirl, dev="postscript", save=TRUE)

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