R: FindA0 specific plot method (original) (raw)
| plot {siggenes} | R Documentation |
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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 |
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| 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 factora0. 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. IfFALSE, 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.