Stability plot.

Produce a ggplot object containing a plot of residual standard deviation against mean count.

Usage

plot_stability(y, x = NULL, design = NULL, bins = 20)

Arguments

y

Transformed counts matrix.

x

Optional, original counts matrix.

design

Matrix specifying a linear model with which to calculate residuals.

bins

Number points in the graph.

Value

A ggplot object.

This must be print()-ed to actually plot.

Details

Genes are partitioned evenly into "bins" bins by average expression level. Mean residual standard deviation is plotted against mean count.

If the variance stabilizing transformation has been successful, this plot should be close to a horizontal line. However it is normal for the standard deviation to drop off for counts below 5.

Author

Paul Harrison