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 Contents]