# MD Plot

### Description

Generates an MD plot for a specified value of Delta.

Contrary to a SAM plot in which the observed values of the test
statistic *D* are plotted against the expected ones, the difference *M*
between the observed and the expected values are plotted against
the observed values in an MD plot.

### Usage

1 2 3 4 |

### Arguments

`object` |
an object of class SAM. |

`delta` |
a numeric value specifying the value of |

`pos.stats` |
an integer between 0 and 2. If |

`sig.col` |
a specification of the color of the significant genes. If |

`xlim` |
a numeric vector of length 2 specifying the x limits (minimum and maximum) of the plot. |

`ylim` |
a numeric vector of length 2 specifying the y limits of the plot. |

`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. |

`xsym` |
should the range of the plotted x-axis be symmetric about the origin? Ignored if |

`ysym` |
should the range of the plotted y-axis be symmetric about the origin? Ignored if |

`forceDelta` |
should the two horizontal lines at |

`includeZero` |
should |

`lab` |
a numeric vector of length 3 specifying the approximate number of tickmarks on the x axis and on the y axis and the label size. |

`pch` |
either an integer specifying a symbol or a single character to be used as the
default in plotting points. For a description of how |

`sig.cex` |
a numerical value giving the amount by which the symbols of the significant genes should be scaled relative to the default. |

`...` |
further graphical parameters. See |

### Value

A MD plot.

### Author(s)

Holger Schwender, holger.schw@gmx.de

### See Also

`sam`

, `sam.plot2`

### Examples

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ```
## Not run:
# Load the package multtest and the data of Golub et al. (1999)
# contained in multtest.
library(multtest)
data(golub)
# Perform a SAM analysis for the two class unpaired case assuming
# unequal variances.
sam.out <- sam(golub, golub.cl, B=100, rand=123)
# Generate a SAM plot for Delta = 2
plot(sam.out, 2)
# As an alternative, the MD plot can be generated.
md.plot(sam.out, 2)
## End(Not run)
``` |

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