Description Usage Arguments Value Author(s) References See Also Examples

Generic function to draw a volcano plot. A volcano plot is a graph that allows to simultaneously assess the P values (statistical significance) and log ratios (biological difference) of differential expression for the given genes.

1 | ```
volcanoPlot(x, y, pointLabels, ...)
``` |

`x` |
either an object of class 'tTest', of class 'limma' or a numeric vector of log ratios, i.e. the log of the fold change values; the names of the logRatio vector will be used to display the names of the most interesting gene |

`y` |
should not be given if an object of class 'tTest' or 'limma' is passed as argument 'x'; if 'x' is a numeric vector of log ratios, 'y' should be given and should be a numeric vector of P-values indicating the statistical significance |

`pointLabels` |
Labels for points on the volcano plot that are interesting taking into account both the x and y dimensions; typically this is a vector of gene symbols; most methods can access the gene symbols directly from the object passed as 'x' argument; the argument allows for custom labels if needed |

`...` |
further arguments to specific methods |

The volcano plot is drawn to the current device.

Tobias Verbeke, based on code by Willem Talloen

Goehlmann, H. and W. Talloen (2009). Gene Expression Studies Using Affymetrix Microarrays, Chapman \& Hall/CRC, pp. 148 - 153.

See `volcanoplotter`

1 2 3 4 5 6 7 | ```
if (require(ALL)){
data(ALL, package = "ALL")
ALL <- addGeneInfo(ALL)
ALL$BTtype <- as.factor(substr(ALL$BT,0,1))
tTestRes <- tTest(object = ALL, groups = "BTtype", probe2gene = TRUE)
volcanoPlot(tTestRes)
}
``` |

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