delta.plot {siggenes}R Documentation

Delta Plots

Description

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

Usage

  delta.plot(object, delta = NULL, helplines = TRUE)

Arguments

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

Details

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.

Value

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

Note

SAM was developed by Tusher et al. (2001).

!!! There is a patent pending for the SAM technology at Stanford University. !!!

Author(s)

Holger Schwender, holger.schw@gmx.de

References

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

See Also

SAM-class,sam

Examples

## 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)

[Package siggenes version 1.4.0 Index]