plot {siggenes} R Documentation

FindA0 specific plot method

Description

Generates a plot of the (logit-transformed) posterior probabilities for a set of values of the fudge factor in an Empirical Bayes Analysis of Microarrays.

Usage

plot(x, y, logit = TRUE, pos.legend = NULL, legend.cex = 0.8, col = NULL,
main = NULL, xlab = NULL, ylab = NULL, only.a0 = FALSE, lty = 1, lwd = 1,
y.intersp = 1.1, ...)

Arguments

 x an object of class FindA0 y the delta value, i.e. the minimum probability for a gene to be called differentially expressed logit should the posterior probabilities be logit-transformed before they are plotted? pos.legend 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. By default, pos.stats=1 if the expression scores can be both positive and negative, and pos.stats=4 if they can only take positive values legend.cex the size of the text in the legend relative to the default size col a vector specifying the colors of the lines for the different values of the fudge factor a0. For a description of how colors are specified, see the help of par 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 only.a0 if TRUE, only the values of a0 are shown in the legend. If FALSE, both the values of a0 and the corresponding numbers of differentially expressed genes are shown lty a value or vector specifying the line type of the curves. For details, see the help of par lwd a numeric value specifying the width of the plotted lines. For details, see the help of par y.intersp a numeric value specifying the space between the rows in the legend ... further graphical parameters for the plot of the posterior probabilities. See the help pages of plot.default and par

Value

a plot of the (logit-transformed) posterior probabilities of the genes for a set of values of the fudge factor

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.