oddsplot {pickgene} | R Documentation |
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).
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)))
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 |
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.
## Not run: oddsplot( x, y ) ## End(Not run)