scaleParameterPlot: Scale parameter plotted against mean intensity

In plw: Probe level Locally moderated Weighted t-tests.

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.

Author(s)

Magnus Astrand

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)

plw documentation built on April 28, 2020, 6:38 p.m.