plot-method {LVSmiRNA}R Documentation

Plot of Residual Variance and Array Effect

Description

Plots results from estVC

Usage

## S4 method for signature 'RA,ANY'
plot(x,Atransf=c("both","sqrt","log"), abline=c("none","rq"),df=3,proportion=.7,
                    col="black",col.rq="red")

Arguments

x

An object of class RA resulting from estVC.

Atransf

Transformation to apply at Array Effect

abline

Add a line to the plot representing a quantile fit

df

Degrees of freedom of the quantile regression

proportion

Quantile to fit

col

Color for plotting points

col.rq

Color for plotting quantile line

Author(s)

Stefano Calza <stefano.calza@biostatistics.it>, Suo Chen and Yudi Pawitan.

References

Calza et al., 'Normalization of oligonucleotide arrays based on the least variant set of genes', (2008, BMCBioinformatics); Pawitan, Y. 'In All Likelihood: Statistical Modeling and Inference Using Likelihood', (2001, Oxford University Press); Huber, P. J., 'Robust estimation of a location parameter', (1964, Annuas of Mathematical Statistics).

See Also

estVC,rq

Examples

## Not run: 

# Starting from an EList object called MIR
data("MIR-spike-in")
AA <- estVC(MIR,method="joint")
plot(AA)
 
## End(Not run)

[Package LVSmiRNA version 1.32.0 Index]