Odds Plot for Differential Microarray Expression

Share:

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

1
2
3
4
oddsplot(x, y, theta, by.level = 10, rotate = FALSE, offset =
         0, main = "", xlab = xlabs, ylab = ylabs, col = NULL,
         cex = c(0.25, 0.75), 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

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

## End(Not run)