The plot method for a MDQC object, which plots ...

Usage

## S3 method for class 'mdqc'
plot(x, levels = c(0.9, 0.95, 0.99), xlab="", ylab="",
mfrow=NULL, mfcol=NULL, ...)

Arguments

x

An object of the class ‘mdqc’.

levels

A vector or scalar between 0 and 1 for displaying
critical values for outliers. See details.

xlab

The label for for x-axis. Note that when there are
multiple plots, the same value of this argument is used for each
one.

ylab

The label for the y-axis. Note that when there are
multiple plots, the same value of this argument is used for each
one.

mfrow

Specify the arrangement of plots on the page, by rows, or
leave NULL to let the function work it out

mfcol

As for mcol, but arrange plots by column instead

...

Other arguments passed to the default plot method.

Details

This plot method is for the output from the function
mdqc, and plots the Mahalanobis distances for each
array. The levels argument plots horizontal lines at critical
values (based on the quantiles of a chi-squard distribution), and aids
in identifying outliers.

For further details, see Cohen Freue et al. (2007)

Cohen Freue, G. V. and Hollander, Z. and Shen, E. and Zamar, R. H. and Balshaw,
R. and Scherer, A. and McManus, B. and Keown, P. and McMaster, W. R. and Ng,
R. T. (2007) ‘MDQC: A New Quality Assessment Method for Microarrays
Based on Quality Control Reports’. Bioinformatics23, 3162 – 3169.

See Also

mdqc

Examples

data(allQC)
mdout <- mdqc(allQC, method="cluster", k=3)
plot(mdout)
## Just one critical value
plot(mdout, levels=0.9)

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.
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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(mdqc)
Loading required package: cluster
Loading required package: MASS
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mdqc/plot.mdqc.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot.mdqc
> ### Title: The plot method for a MDQC object
> ### Aliases: plot.mdqc
> ### Keywords: multivariate robust
>
> ### ** Examples
>
> data(allQC)
> mdout <- mdqc(allQC, method="cluster", k=3)
> plot(mdout)
>
> ## Just one critical value
> plot(mdout, levels=0.9)
>
>
>
>
>
> dev.off()
null device
1
>