delta.plot {siggenes} | R Documentation |
Generates both a plot of Delta vs. the FDR and a plot of Delta vs. the number of identified genes in a SAM analysis.
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.
## 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)