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.

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.

`em.ggb`
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