The function plots contours for the odds that points on microarray show differential expression between two conditions (e.g. Cy3 and Cy5 dye channels on the same microarray).

1 2 3 4 |

`x` |
first condition expression levels |

`y` |
second condition expression levels |

`theta` |
four parameters from |

`by.level` |
odds plot contours increase by this level |

`rotate` |
rotate to average versus ratio if TRUE, otherwise plot conditions against each other |

`offset` |
offset for |

`main` |
main title for plot |

`xlab` |
horizontal axis label (default if |

`ylab` |
vertical axis label (default if |

`col` |
color of points (if NULL, use black for non-changing points, blue for changing points) |

`cex` |
character expansion (use |

`shrink` |
use shrinkage on expression levels if TRUE (default is FALSE) |

`lims` |
limits for plot area |

Fit Gamma/Gamma/Bernoulli model (equal marginal distributions) The model has spot intensities x ~ Gamma(a,b); y ~ Gamma(a,c). The shape parameters b and c are ~ Gamma(a0,nu). With probability p, b = c; otherwise b != c. All spots are assumed to be independent.

Log odds for all points in original order.

Michael Newton

MA Newton, CM Kendziorski, CS Richmond, FR Blattner and KW
Tsui (2000) “On differential variability of expression ratios:
improving statistical inference about gene expression changes from
microarray data,”
*J Computational Biology 00*: 000-000.

1 2 3 4 | ```
## Not run:
oddsplot( x, y )
## End(Not run)
``` |

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