The function boxplot produces boxplots of microarray spot
statistics for the classes "marrayRaw",
"marrayNorm".
We encourage users to use boxplot rather than maBoxplot.
The name of the arguments have changed slightly.
Usage
## S4 method for signature 'marrayRaw'
boxplot(x, xvar="maPrintTip", yvar="maM", ...)
## S4 method for signature 'marrayNorm'
boxplot(x, xvar="maPrintTip", yvar="maM", ...)
Arguments
x
Microarray object of class "marrayRaw", "marrayNorm"
xvar
Name of accessor method for the spot statistic used to
stratify the data, typically a slot name for the microarray layout
object (see "marrayLayout") such as maPlate or
a method such as maPrintTip. If x is NULL, the data
are not stratified.
yvar
Name of accessor method for the spot statistic of
interest, typically a slot name for the microarray object m,
such as maM.
...
Optional graphical parameters, see par.
Details
If there are more than one array in the batch, the function produces a
boxplot for each array in the batch. Such plots are useful when
assessing the need for between array normalization, for example, to deal
with scale differences among different arrays. Default graphical
parameters are chosen for convenience using the function
maDefaultPar (e.g. color palette, axis labels, plot
title) but the user has the option to overwrite these parameters at any
point.
Author(s)
Jean Yang and Sandrine Dudoit
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
maBoxplot, maDefaultPar.
Examples
# To see the demo type demo(marrayPlots)
# Examples use swirl dataset, for description type ? swirl
data(swirl)
# Boxplots of pre-normalization log-ratios M for each of the 16
# print-tip-groups for the Swirl 93 array.
# - Default arguments
boxplot(swirl[,3])
# All spots
boxplot(swirl[,3], xvar=NULL, col="green")
# Boxplots of pre-normalization red foreground intensities for each grid row
# for the Swirl 81 array.
boxplot(swirl[,1], xvar="maGridRow", yvar = "maRf", main = "Swirl array 81: pre-normalization red foreground intensity")
# Boxplots of pre-normalization log-ratios for each array in swirl
boxplot(swirl, main="Swirl arrays: pre-normalization log-ratios")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(marray)
Loading required package: limma
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/marray/boxplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: boxplot
> ### Title: Boxplots for cDNA microarray spot statistics
> ### Aliases: boxplot,marrayRaw-method boxplot,marrayNorm-method
> ### Keywords: hplot
>
> ### ** Examples
>
>
> # To see the demo type demo(marrayPlots)
>
> # Examples use swirl dataset, for description type ? swirl
> data(swirl)
>
> # Boxplots of pre-normalization log-ratios M for each of the 16
> # print-tip-groups for the Swirl 93 array.
> # - Default arguments
> boxplot(swirl[,3])
>
> # All spots
> boxplot(swirl[,3], xvar=NULL, col="green")
>
> # Boxplots of pre-normalization red foreground intensities for each grid row
> # for the Swirl 81 array.
> boxplot(swirl[,1], xvar="maGridRow", yvar = "maRf", main = "Swirl array 81: pre-normalization red foreground intensity")
>
> # Boxplots of pre-normalization log-ratios for each array in swirl
> boxplot(swirl, main="Swirl arrays: pre-normalization log-ratios")
>
>
>
>
>
> dev.off()
null device
1
>