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 nonchanging 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: 000000.
1 2 3 4  ## Not run:
oddsplot( x, y )
## End(Not run)

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