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 = FALSE)

### 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.

### 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 1.64.0 Index]