oddsplot {pickgene} | R Documentation |

## Odds Plot for Differential Microarray Expression

### Description

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).

### Usage

oddsplot(x, y, theta, by.level = 10, rotate = FALSE, offset = 0,
main="", xlab = <<see below>>, ylab = <<see below>>,
col=<<see below>>, cex = <<see below>>,
shrink = FALSE, lims = range( c( x, y )))

### Arguments

`x` |
first condition expression levels |

`y` |
second condition expression levels |

`theta` |
four parameters from `em.ggb` |

`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 `log` transform |

`main` |
main title for plot |

`xlab` |
horizontal axis label (default if `Cy3` if
`rotate` is FALSE, `Average Intensity` otherwise |

`ylab` |
vertical axis label (default if `Cy5` if
`rotate` is FALSE, `Cy3 / Cy5` otherwise |

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

`cex` |
character expansion (use `rep(.25,2)` to have all points the
same size) |

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

`lims` |
limits for plot area |

### Details

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.

### Value

Log odds for all points in original order.

### Author(s)

Michael Newton

### References

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.

### See Also

`em.ggb`

### Examples

## Not run:
oddsplot( x, y )
## End(Not run)

[Package

*pickgene* version 1.0.0

Index]