oddsplot: Odds Plot for Differential Microarray Expression

In pickgene: Adaptive Gene Picking for Microarray Expression Data Analysis

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 = 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

## Not run: 
oddsplot( x, y )

## End(Not run)

pickgene documentation built on Nov. 8, 2020, 6:50 p.m.