maDiagnPlots1 {marrayPlots} | R Documentation |
These three functions produce sets of basic diagnostic plots for pre– and post–normalization cDNA microarray data.
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"))
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". |
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.
This function maynot work properly when "save=FALSE".
Sandrine Dudoit, http://www.stat.berkeley.edu/~sandrine, Yee Hwa (Jean) Yang.
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.
library(marrayNorm) # Examples use swirl dataset, for description type ? swirl data(swirl) maPlate(swirl)<-maCompPlate(swirl,384) # Pre-normalization maRawPlots(swirl[,3]) # Post-normalization mnorm<-maNorm(swirl[,3], norm="twoD") maNormPlots(mnorm, title="Swirl array 93 -- 2D normalization")