| plot {siggenes} | R Documentation |
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.
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, ...)
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 |
a plot of the (logit-transformed) posterior probabilities of the genes for a set of values of the fudge factor
Holger Schwender, [email protected]
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.