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.
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)