meanSdPlot {vsn}R Documentation

Plot row standard deviations versus row means

Description

Methods for objects of classes matrix, ExpressionSet and vsn to plot row standard deviations versus row means.

Usage

meanSdPlot(x, 
           ranks = TRUE,
           xlab  = ifelse(ranks, "rank(mean)", "mean"),
           ylab  = "sd",
           pch   = ".",
           plot  = TRUE,
           ...)

Arguments

x An object of class matrix, ExpressionSet, or vsn.
ranks Logical, indicating whether the x-axis (means) should be plotted on the original scale (FALSE) or on the rank scale (TRUE). The latter distributes the data more evenly along the x-axis and allows a better visual assessment of the standard deviation as a function of the mean.
xlab Character, label for the x-axis.
ylab Character, label for the y-axis.
pch Plot symbol.
plot Logical. If TRUE (default), a plot is produced. Calling the function with plot=FALSE can be useful if only its return value is of interest.
... Further arguments that get passed to plot.default.

Details

Standard deviation and mean are calculated row-wise from the expression matrix (in) x. The scatterplot of these versus each other allows to visually verify whether there is a dependence of the standard deviation (or variance) on the mean. The red dots depict the running median estimator (window-width 10%). If there is no variance-mean dependence, then the line formed by the red dots should be approximately horizontal.

Value

A named list with two components, containing x-positions and values of the running median estimator (the red dots in the plot). The methods can also have a side effect, which is to create a plot on the active graphics device.

Author(s)

Wolfgang Huber http://www.ebi.ac.uk/huber

See Also

vsn

Examples

  data(kidney)
  log.na = function(x) log(ifelse(x>0, x, NA))

  exprs(kidney) = log.na(exprs(kidney))
  meanSdPlot(kidney)

  ## ...try this out with non-logged data, the lymphoma data, your data...

[Package vsn version 3.8.0 Index]