scaleParameterPlot {plw} | R Documentation |
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.
scaleParameterPlot(model,main="Scale parameter curve", col=1,pch='.',lty=1,curveCol=2,knotsPch=19,knotsCol=3)
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. |
Magnus Astrand
plw, lmw
# ------------------------------------------ # 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)