maDiagnPlots1 {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

maDiagnPlots1(mraw, title=NULL, save=TRUE,
        fname=paste(as.character(maLabels(maTargets(mraw))[1]), ".ps", sep = ""), 
        dev=c("postscript", "jpeg"))

maRawPlots(mraw, title=NULL, save = TRUE, 
        fname = paste(as.character(maLabels(maTargets(mraw))[1]), ".ps", sep = ""), 
        dev = c("postscript", "jpeg"))

maNormPlots(mnorm, title=NULL, save = TRUE, 
        fname = paste(as.character(maLabels(maTargets(mnorm))[1]),".ps", sep = ""), 
        dev = c("postscript", "jpeg"))

Arguments

mraw Microarray object of class "marrayRaw", for maDiagnPlots1 maRawPlots. By default, plots are done for the first array in the batch.
mnorm Microarray object of class "marrayNorm", for maNormPlots. By default, plots are done for the first array in the batch.
title A "character" string for the plot title. If NULL a default title is shown.
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, "postscript" or "jpeg".

Details

maDiagnPlots1 produces eight plots of pre– and post–normalization cDNA microarray data: color images of Cy3 and Cy5 background intensities, and of pre– and post–normalization log–ratios M; boxplots of pre– and post–normalization log–ratios M by print–tip–group; MA–plots of pre– and post–normalization log–ratios M by print–tip–group.

maRawPlots produces six plots of pre–normalization cDNA microarray data: color images of Cy3 and Cy5 background intensities and log–ratios M; boxplots of log–ratios M by print–tip–group and plate; MA–plot of log–ratios M by print–tip–group.

maNormPlots produces four plots of post–normalization cDNA microarray data: color images of location normalization values Mloc and normalized log–ratios M; boxplots of normalized log–ratios M by print–tip–group; MA–plot of normalized log–ratios M by print–tip–group.

Note

This function maynot work properly when "save=FALSE".

Author(s)

Sandrine Dudoit, http://www.stat.berkeley.edu/~sandrine, Yee Hwa (Jean) Yang.

References

S. Dudoit and Y. H. Yang. (2002). Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger, editors, The Analysis of Gene Expression Data: Methods and Software, Springer, New York.

See Also

maPlot, maBoxplot, maImage.

Examples

# Examples use swirl dataset, for description type ? swirl
data(swirl)

maPlate(swirl)<-maCompPlate(swirl,384)

# Pre-normalization
maRawPlots(swirl)

# Post-normalization
mnorm<-maNorm(swirl[,3], norm="twoD")
maNormPlots(mnorm, title="Swirl array 93 -- 2D normalization")


[Package marray version 1.5.14 Index]