plot.t2: Diagnostic Plots for Two-Sample t-statistics

In gnyamundanda/sma: Statistical Microarray Analysis

Description

Plots of two-sample t-statistics, |t-numerator| and t-denominator against average A, and plot of |t-numerator| against t-denominator. For each spot on a given slide, A = log_2(R*G)/2, where (R,G) denotes the red and green fluorescence intensity pair. Points with t-statistics exceeding user defined thresholds are highlighted.

Usage

plot.t2(x, main.title="T plots", low=-5, high=5,...)

Arguments

x	output from the function stat.t2.
main.title	title for the plot.
low	lower threshold for t-statistic: points with t<low are colored in green.
high	upper threshold for t-statistic: points with t>high are colored in red.
...	additional graphical parameters

Author(s)

Sandrine Dudoit, [e-mail]
Yee Hwa Yang, [e-mail]

See Also

stat.t2, t2stat.func, plot, t.test.

Examples

data(MouseArray)
# mouse.setup <- init.grid()
# mouse.data <- init.data() ## see \emph{init.data}
# mouse.lratio <- stat.ma(mouse.data, mouse.setup)

## Calculation of t-statistics
## cl <- c(rep(1,3), rep(2,3))
## mouse.t2 <- stat.t2(mouse.lratio, cl)

## Diagnostic plots
plot.t2(mouse.t2, "Mouse")

gnyamundanda/sma documentation built on May 3, 2019, 5:17 p.m.