scaleParameterPlot {plw} | R Documentation

## 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.

### 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)

[Package plw version 1.2.0 Index]