delta.plot: Delta Plots
In siggenes: Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Description Usage Arguments Details Value Author(s) References See Also Examples

Generates both a plot of Delta vs. the FDR and a plot of Delta vs.\ the number of identified genes in a SAM analysis.

1	delta.plot(object, delta = NULL, helplines = FALSE)

`object`	a object of class SAM.
`delta`	a vector of values for Delta. If `NULL`, a default set of Delta values will be used.
`helplines`	if `TRUE`, help lines will be drawn in the Delta plots.

The Delta plots are a visualization of the table generated by sam that contains the estimated FDR and the number of identified genes for a set of Delta values.

Two plots in one graphsheet: The plot of Delta vs. FDR and the plot of Delta vs. the number of identified genes.

Holger Schwender, holger.schw@gmx.de

Tusher, V., Tibshirani, R., and Chu, G. (2001). Significance Analysis of Microarrays Applied to the Ionizing Radiation Response. PNAS, 98, 5116-5121.

SAM-class,sam

## Not run: 
  # Load the package multtest and the data of Golub et al. (1999)
  # contained in multtest.
  library(multtest)
  data(golub)

  # Perform a SAM analysis.
  sam.out<-sam(golub, golub.cl, B=100, rand=123)
  
  # Generate the Delta plots for the default set of Deltas computed by sam.
  delta.plot(sam.out)
  
  # Another way of generating the same plot.
  plot(sam.out)

  # Generate the Delta plots for Delta = 0.2, 0.4, ..., 2.
  plot(sam.out, seq(0.2, 2, 0.2))

## End(Not run)