plw (version 1.30.0)

scaleParameterPlot: Scale parameter plotted against mean intensity

Description

Will produce a scatter plot of variance estimators (logged) for each probe (probe set) against the corresponding mean intensity together with the fitted scale-parameter curve and points showing the knots of the used spline.

Usage

scaleParameterPlot(model,main="Scale parameter curve", col=1,pch='.',lty=1,curveCol=2,knotsPch=19,knotsCol=3)

Arguments

model

On object obtained from the function plw or lmw.

main

Main title of plot.

col

Color for individual points (mean,logs2).

pch

Plot symbol for individual points (mean,logs2).

lty

Line type for fitted scale parameter curve.

curveCol

Line color for fitted scale parameter curve.

knotsPch

Plot symbol for spline knots.

knotsCol

Plot color for spline knots.

See Also

plw, lmw

Examples

# ------------------------------------------
# Example using the result of the analysis of
# the 6 arrays in the AffySpikeU95Subset data set

# Loading the data
data(AffySpikeU95Subset)

# Defining design and contrast matrix
group<-factor(rep(1:2,each=3))
design<-model.matrix(~group-1)
contrast<-matrix(c(1,-1),1,2)

# Analyzing using plw
model1<-plw(AffySpikeU95Subset,design=design,contrast=contrast,
            epsilon=0.01)

## Look at fitted curve for scale parameter
scaleParameterPlot(model1)