plot {siggenes}R Documentation

EBAM specific plot method

Description

Generates a plot of the posterior probabilities given by an object of class EBAM.

Usage

   plot(x, y, pos.stats = 2, sig.col = 3, sig.cex = 1, pch = NULL, stats.cex = 0.8,
        main = NULL, xlab = NULL, ylab = NULL, y.intersp = 1.3, ...)

Arguments

x an object of class EBAM
y the delta value, i.e. the minimum probability for a gene to be called differentially expressed
pos.stats an integer between 0 and 4. If pos.stats=1, general information as the number of significant genes and the estimated FDR for the specified value of y will be plotted in the upper center of the plot. If pos.stats=2, these information will be plotted in the bottom right corner, if pos.stats=3 in the bottom left corner, and if pos.stats=4 in the upper left corner. If pos.stats=0, no information will be plotted
sig.col a specification of the color of the significant genes. For a description of how colors are specified, see the help of par
sig.cex a numeric value giving the amount by which the symbols of the significant genes should be scaled relative to the default
pch either an integer specifying a symbol or a single character to be used as the default in plotting points. For a description of how pch can be specified, see the help of par
stats.cex the size of the statistics printed in the plot relative to the default size
main a character string naming the main title of the plot
xlab a character string naming the label of the x axis
ylab a character string naming the label of the y axis
y.intersp a numeric value specifying the space between the rows in which the statistics are plotted
... further graphical parameters for the EBAM plot. See the help pages of plot.default and par

Value

a plot of the posterior probabilities of the genes for a specified value of delta

Author(s)

Holger Schwender, holger.schw@gmx.de

References

Efron, B., Tibshirani, R., Storey, J.D. and Tusher, V. (2001). Empirical Bayes Analysis of a Microarray Experiment, JASA, 96, 1151-1160.

Schwender, H., Krause, A. and Ickstadt, K. (2003). Comparison of the Empirical Bayes and the Significance Analysis of Microarrays. Technical Report, SFB 475, University of Dortmund, Germany.