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)

[Package marray version 1.5.14 Index]