maDiagnPlots {marray} | R Documentation |
These three functions produce sets of basic diagnostic plots for pre- and post-normalization cDNA microarray data.
maDiagnPlots(mraw, mNorm = NULL, save = TRUE, fname = NULL, dev= "png", pch, col, DEBUG = FALSE, ...)
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'. |
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.
This function may not work properly when "save=FALSE".
Yee Hwa (Jean) Yang
data(swirl) ## maDiagnPlots(swirl, dev="postscript", save=TRUE)