plotRA: Plot of Residual Variance and Array Effect

In LVSmiRNA: LVS normalization for Agilent miRNA data

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 <[e-mail]>, 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)

LVSmiRNA documentation built on Oct. 31, 2019, 5:29 a.m.