plot.mdqc: The plot method for a MDQC object

Description

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

Usage

"plot"(x, levels = c(0.9, 0.95, 0.99), xlab="", ylab="",
mfrow=NULL, mfcol=NULL, ...)

Arguments

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)

References

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’. Bioinformatics 23, 3162 -- 3169.

Examples

Run this code

data(allQC)
mdout <- mdqc(allQC, method="cluster", k=3)
plot(mdout)

## Just one critical value
plot(mdout, levels=0.9)