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.